RU2575605C2 - Genetic markers, associated with corn drought resistance - Google Patents

Abstract

FIELD: chemistry.

SUBSTANCE: invention relates to biochemistry. Described is method for obtaining corn plant with improved optimisation of water consumption and plant thereof obtained.

EFFECT: invention makes it possible to obtain plants, possessing higher drought resistance.

14 cl, 6 dwg, 13 tbl, 13 ex

Description

The subject matter disclosed herein claims priority to provisional patent application Serial No. 61/289,718 filed December 23, 2009 and provisional patent application Serial No. 61/369,999 filed August 2, 2010, each of which are incorporated herein by reference in full.

FIELD OF THE INVENTION

An object of the invention disclosed herein relates to corn, such as maize of the Zea mays species, and methods for breeding this species. More specifically, an object of the invention disclosed herein relates to maize lines, such as Zea mays lines, with one or more genotypes with improved optimization of water consumption, as well as methods for breeding this species, and in some embodiments of the invention, the methods include analysis of genetic markers and / or nucleic acid sequence analysis.

BACKGROUND

Drought is one of the main factors limiting corn production in the world - 15% of the world corn crop is lost every year due to drought. Periods of drought can occur at any time during the growing season, but corn is especially sensitive to drought in the period before and during flowering. If drought occurs during such a critical period, it can lead to a significant decrease in grain yield.

Identification of genes that increase drought tolerance of maize can lead to more efficient crop production, making it possible to identify, select and produce maize with increased drought tolerance. Thus, the goal of plant breeding is to combine various desirable traits in one plant. For field crops such as corn, such traits may include greater yield and better agronomic quality. However, genetic loci that affect yield and agronomic quality are not always known, and even if they are known, their contribution to such traits is often unclear. Thus, it is necessary to identify new loci that can positively influence such desirable traits, and / or it is necessary to detect the possibilities for such an effect at known loci.

Once discovered, such desired loci can be selected as part of a breeding program in order to obtain plants bearing the desired traits. An example of an embodiment of a method for generating such plants includes the transfer of nucleic acid sequences by introgression from plants that possess the desired genetic information to plants that do not possess it by crossing plants using traditional breeding methods. Desired loci can be introgressed into commercially available plant varieties using marker selection (MAS) or marker crossing (MAB). MAS and MAB suggest the use of one or more molecular markers to identify and select such offspring plants that contain one or more loci encoding the desired traits. Such identification and selection may be based on the selection of informative markers associated with the desired traits. MAV can also be used to produce nearly isogenic lines (NIL) carrying loci of interest, allowing a more detailed study of the effect that each locus can have on the desired trait, and is also an effective way to obtain populations using inbreeding of inbred lines (BIL) .

Drought during the cultivation of corn is one of the main factors limiting the production of corn in the world. If drought occurs immediately before or during flowering, it can lead to an increase in the length of time between flowering and sweeping of pistillate columns and a decrease in grain yield. 15% of world corn or more than 19 million tons is lost annually due to drought. Identification of candidate genes that can improve the drought tolerance of maize crops can lead to more efficient agricultural production in the affected areas.

What is really needed is new methods and compositions for the genetic analysis of Zea mays varieties with respect to drought tolerance and for applying the information obtained to obtain new Zea mays plants that have improved signs of optimizing water consumption.

SUMMARY OF THE INVENTION

This section, containing the essence of the invention, lists several embodiments of the disclosed object of the invention and in many cases lists the variations and permutations of these embodiments of the invention. The present section on the subject matter of the invention is merely exemplified of numerous and varied embodiments of the invention. Mention of one or more characteristic features of this embodiment of the invention is also given as an example. A similar embodiment of the invention can usually exist with or without the mentioned feature (s), similarly, these features can be applied to other embodiments of the disclosed invention, regardless of whether they are listed in this section regarding the invention, or no. To avoid excessive repetition, this section does not list or offer all possible combinations of such features.

The present invention relates to compositions and methods for identifying, breeding and producing maize with increased drought tolerance. The present invention also relates to a drought tolerant corn plant or germplasm.

Some embodiments of the invention relate to methods for identifying a drought tolerant corn plant or germplasm. Such methods may comprise detecting in a corn plant or germplasm a marker associated with increased drought tolerance.

Some embodiments of the invention relate to methods for producing a drought tolerant corn plant. Such methods may comprise detecting in the corn germplasm the presence of a marker associated with increased drought tolerance, and producing a progeny plant from said corn germplasm.

In some embodiments, the presence of a marker associated with increased drought tolerance is detected using a marker probe. In some such embodiments, the presence of a marker associated with increased drought tolerance is detected in the amplification product from a nucleic acid sample isolated from a corn plant or germplasm. In some embodiments of the invention, the marker contains a haplotype, and many probes are used to detect the alleles that make up the haplotype. In some such embodiments, the alleles that make up the haplotype are found in a variety of amplification products from a nucleic acid sample isolated from a corn plant or germplasm.

Some embodiments of the invention relate to methods for selecting a drought tolerant corn plant or germplasm. Such methods may include crossing a first corn plant or germplasm with a second corn plant or germplasm, the first corn plant or germplasm containing a marker associated with increased drought tolerance and selecting a descendant plant or germplasm that possesses this marker.

Some embodiments of the invention relate to methods of introgression of an allele associated with increased drought tolerance into a corn plant or germplasm. Such methods may include crossbreeding a first corn plant or germplasm containing an allele associated with increased drought tolerance with a second corn plant or germplasm lacking said allele and re-crossbreeding progeny plants containing said allele with a second corn plant or germinal plasma to produce drought resistant corn plants or germplasm containing the allele associated with increased drought tolerance. Offspring containing an allele associated with increased drought tolerance can be identified by the presence in their genomes of the presence of a marker associated with the allele.

The present invention also relates to corn plants and / or germplasm identified, produced or selected by any of the methods of the invention, as well as any offspring or seeds obtained from a corn plant or germplasm identified, produced or selected using these methods.

The present invention also relates to non-naturally occurring corn plants and / or germplasm containing one or more markers associated with increased drought tolerance.

The present invention also relates to isolated and / or purified markers associated with increased drought tolerance. Such markers may contain a nucleotide sequence that is at least 85%, 90%, 95% or 99% identical to any of the sequences of SEQ ID NO: 1-117, 400 and 401, their inverse complementary sequence, or their informative or functional fragments .

The present invention also relates to compositions containing a pair of primers capable of amplifying a nucleic acid sample isolated from a corn plant or germplasm to create a marker associated with increased drought tolerance. Such compositions may contain, consist essentially of, or consist of one of the pairs of amplification primers listed in Table 1.

Table 1 SEO ID NO examples of oligonucleotide primers that can be used to analyze loci, alleles and haplotypes of water consumption optimization Genomic locus Examples of amplification primers Examples of analysis primers 1, 61 118, 119 232, 233 2, 63 120, 121 346, 347; 348, 349 3, 63 122, 123 234, 235 4, 64 124, 125 236, 237 5, 65 126, 127 238, 239 6, 66 128, 129 240, 241 7, 67 130, 131 242, 243; 244, 245; 246, 247; 248, 249; 250, 251; 350, 351; 352,353; 8, 68 132, 133 252, 253 9, 69 134, 135 254, 255 10, 70 136, 137 256, 257 11, 71 138, 139 258, 259 12, 13, 72 140, 141 260, 261; 262, 263; 264, 265; 266, 267 14, 73 142, 143 268, 269 15, 74 144, 145 270, 271 16, 75 146, 147 272, 273 17, 76 148, 149 274, 275 18, 77 150, 151 276, 277 19, 78 152, 153 278, 279; 280, 281; 282, 283; 354, 355; 356, 357 20, 79 154, 155 284, 285 21, 80 156, 157 286, 287 22, 81 158, 159 288, 289 23, 82 160, 161 358, 359; 360, 361 24, 83 162, 163 362, 363 25, 84 164, 165 290, 291; 364, 365 26, 85 166, 167 366, 367 27, 86 168, 169 292, 293 368, 369 28, 87 170, 171 294, 295 29, 88 172, 173 370, 371 30, 89 174, 175 296, 297; 298, 299 31, 90 176, 177 300, 301 32, 91 178, 179 302, 303 33, 92 180, 181 372, 373 34, 93 182, 183 304, 305; 306, 307; 308, 309 35, 94 184, 185 310, 311 36, 95 186, 187 312, 313 37, 96 188, 189 314, 315; 316, 317 38, 97 190, 191 318, 319; 320, 321 39, 98 192, 193 322, 323 40, 99 194, 195 324, 325 41, 100 196, 197 326, 327; 328, 329 42, 101 198, 199 330, 331 43, 102 200, 201 332, 333 44, 45, 103 202, 203 374,375; 376, 377 46, 104 204, 205 378, 379 47, 105 206, 207 380, 381 48, 106 208, 209 382, 383 49, 107 210, 211 334, 335 50, 51, 108 212, 213 336, 337; 384, 385 52, 109 214, 215 338, 339 53, 110 216, 217 340, 341 54, 111 218, 219 344, 345 55, 112 220, 221 386, 387 56, 113 222, 223 388, 389; 390, 391 57, 114 224, 225 392, 393 58, 115 226, 227 394, 395 59, 116 228, 229 396, 397 60, 117 230, 231 398, 399 400, 401 402, 407 408, 409; 410, 411; 412, 413

The marker associated with increased drought tolerance may comprise, consist essentially of, or consist of one allele or combination of alleles at one or more genetic loci.

Thus, some embodiments of the disclosed subject matter relate to methods for producing hybrid plants with improved optimization of water consumption. In some embodiments of the invention, the method comprises: (a) providing a first plant containing a first genotype containing any of haplotypes AM, (b) providing a second plant containing a second genotype containing any of haplotypes AM, wherein the second plant contains at least one of the haplotypes AM that is not present in the first plant, (c) crossing the first plant and the second corn plant to obtain generation F1, identifying one or more members of the F1 generation that contains the desired a genotype containing any combination of AM haplotypes, the desired genotype being different from both the first genotype (a) and the second genotype (b), whereby a hybrid plant is produced with improved optimization of water consumption. In some embodiments, haplotypes AM are defined as follows:

i) haplotype A contains nucleotide G at a position that corresponds to position 115 of the sequence SEQ ID NO: 1, nucleotide A at a position that corresponds to position 270 of SEQ ID NO: 1, nucleotide T at a position that corresponds to position 301 of SEQ ID NO: 1 and nucleotide A at the position that corresponds to position 483 of SEQ ID NO: 1 on chromosome 8 in the genome of the first plant;

ii) haplotype B contains a deletion at positions 4497-4498 of the sequence SEQ ID NO: 7, nucleotide G at the position corresponding to position 4505 of the sequence SEQ ID NO: 7, nucleotide T at the position corresponding to position 4609 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4792 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4836 of the sequence SEQ ID NO: 7, nucleotide C in a position that matches the positions and 4844 of SEQ ID NO: 7, nucleotide G at a position that corresponds to position 4969 of SEQ ID NO: 7, and TCC trinucleotide at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7 on chromosome 8 in the genome of the first plant ;

iii) haplotype C contains nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 8, nucleotide G at the position that corresponds to position 390 of the sequence SEQ ID NO: 8, and nucleotide A at the position that corresponds to position 477 of the sequence SEQ ID NO: 8 on chromosome 2 in the genome of the first plant;

iv) haplotype D contains nucleotide G at the position that corresponds to position 182 of the sequence SEQ ID NO: 19, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 330 of the sequence SEQ ID NO: 19 : 19, and nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19 on chromosome 8 in the genome of the first plant;

v) haplotype E contains nucleotide C at a position that corresponds to position 61 of the sequence SEQ ID NO: 21, nucleotide C at a position that corresponds to position 200 of the sequence SEQ ID NO: 21, and a deletion of nine nucleotides at positions that correspond to positions 316-324 the sequence of SEQ ID NO: 21 on chromosome 5 in the genome of the first plant;

vi) haplotype F contains nucleotide G at the position corresponding to position 64 of the sequence SEQ ID NO: 27 and nucleotide T at the position corresponding to position 254 of the sequence SEQ ID NO: 27 on chromosome 8 in the genome of the first plant;

vii) haplotype G contains nucleotide C at the position corresponding to position 98 of the sequence SEQ ID NO: 28, nucleotide T at the position corresponding to position 147 of the sequence SEQ ID NO: 28, nucleotide C at the position which corresponds to position 224 of the sequence SEQ ID NO: : 28, and nucleotide T at the position that corresponds to position 496 of the sequence SEQ ID NO: 28 on chromosome 9 in the genome of the first plant;

viii) haplotype H contains nucleotide T at a position that corresponds to position 259 of the sequence SEQ ID NO: 30, nucleotide T at the position that corresponds to position 306 of the sequence SEQ ID NO: 30, nucleotide A at the position that corresponds to position 398 of the sequence SEQ ID NO : 30, and nucleotide C at the position that corresponds to position 1057 of the sequence SEQ ID NO: 30 on chromosome 4 in the genome of the first plant;

ix) haplotype I contains nucleotide C at a position that corresponds to position 500 of the sequence SEQ ID NO: 36, nucleotide G at the position that corresponds to position 568 of the sequence SEQ ID NO: 36, and nucleotide T at the position that corresponds to position 698 of the sequence SEQ ID NO: 36 on chromosome 6 in the genome of the first plant;

x) haplotype J contains nucleotide A at the position that corresponds to position 238 of the sequence SEQ ID NO: 42, a deletion of nucleotides that correspond to positions 266-268 of the sequence SEQ ID NO: 42, and nucleotide C at the position that corresponds to position 808 of the sequence SEQ ID NO: 42 in the genome of the first plant;

xi) haplotype K contains nucleotide C at the position that corresponds to position 166 of the sequence SEQ ID NO: 49, and nucleotide A at the position that corresponds to position 224 of the sequence SEQ ID NO: 49, nucleotide G at the position that corresponds to position 650 of the sequence SEQ ID NO: 49, and nucleotide G at the position that corresponds to position 892 of the sequence SEQ ID NO: 49 on chromosome 8 in the genome of the first plant;

xii) haplotype L contains nucleotide C at positions that correspond to positions 83, 428, 491 and 548 of the sequence SEQ ID NO: 53 on chromosome 9 in the genome of the first plant, and

xiii) haplotype M contains nucleotide C at the position that corresponds to position 83 in the sequence of SEQ ID NO: 400, nucleotide A at the position that corresponds to position 119 of the sequence SEQ ID NO: 400, and nucleotide T at the position that corresponds to position 601 of the sequence SEQ ID NO: 400.

In some embodiments of the invention, a hybrid plant with improved optimization of water consumption contains each of the haplotypes AM that are present in the first plant, as well as at least one additional haplotype selected from the haplotypes AM that is present in the second plant. In some embodiments, the first plant is a recurrent parent containing at least one of haplotypes AM, and the second plant is a donor that contains at least one of haplotypes AM that is not in the first plant. In some embodiments, the first plant is homozygous for at least two, three, four, or five haplotypes AM. In some embodiments of the invention, the hybrid plant contains at least three, four, five, six, seven, eight, or nine haplotypes AM.

In some embodiments, the identification comprises genotyping one or more members of the F1 generation, obtained by crossing the first plant and the second plant, with respect to each of the haplotypes present in the first plant or in the second plant.

In some embodiments, the first plant and the second plant are Zea mays plants.

In some embodiments of the invention, improved optimization of water consumption provides an increased or stable yield in a water-deficient environment compared to a control plant. In some embodiments of the invention, a hybrid with improved optimization of water consumption can be sown with a higher density of sowing. In some embodiments of the invention, a hybrid with improved optimization of water consumption does not exhibit gene drag-induced yield linkage when grown under favorable humidity conditions.

In some embodiments, an object of the invention disclosed herein also relates to Zea mays hybrid plants produced by the methods disclosed herein, or to their cell, tissue culture, seed, or parts.

In some embodiments, an object of the invention disclosed herein also relates to Zea mays inbred plants produced by crossbreeding and / or selfing and / or the production of double haploids from Zea mays hybrid plants disclosed herein, or to their cell, tissue culture, seed , or parts.

In some embodiments, an object of the invention disclosed herein also relates to Zea mays inbred or hybrid plants whose genome contains at least three, four, five, six, seven, eight, or nine haplotypes AM, wherein haplotypes AM associated with the optimization of water consumption and are defined in this document. In some embodiments, the Zea mays inbred or hybrid plant comprises a genome containing haplotypes C, D, and G; haplotypes C, D and L; haplotypes C, G, H; haplotypes C, G and I; haplotypes C, I and L; haplotypes E, G, and I; haplotypes F, G and H; haplotypes A, C, F and G; haplotypes C, E, H and I; haplotypes C, G, H, and I; haplotypes C, H, I and K; haplotypes C, H, I and L; haplotypes E, F, G and H; haplotypes A, C, G, H and I; haplotypes B, C, D, G and L; haplotypes C, E, G, H and I; haplotypes C, G, H, I and L; haplotypes A, C, G, H, I and K; haplotypes C, E, F, G, H, I, J, K and L; haplotypes C, D, G and M; haplotypes C, D, L and M; haplotypes C, G, H and M; haplotypes C, G, I and M; haplotypes C, I, L and M; haplotypes E, G, I and M; haplotypes F, G, H and M; haplotypes A, C, F, G and M; haplotypes C, E, H, I and M; haplotypes C, G, H, I and M; haplotypes C, H, I, K and M; haplotypes C, H, I, L and M; haplotypes E, F, G, H and M; haplotypes A, C, G, H, I and M; haplotypes B, C, D, G, L and M; haplotypes C, E, G, H, I and M; haplotypes C, G, H, I, L and M; haplotypes A, C, G, H, I, K, and M; and haplotypes C, E, F, G, H, I, J, K, L, and M. In some embodiments, an inbred or hybrid Zea mays plant is a hybrid a plant that is homozygous for at least one of AM haplotypes.

In some embodiments, the Zea mays inbred or hybrid plant comprises a genome comprising haplotypes A, C, E, G, H, and I, optionally further comprising haplotype M; haplotypes B, C, D, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H and L, optionally additionally containing haplotype M; haplotypes B, C, D, G, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I, and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G and H, optionally additionally containing haplotype M; haplotypes D, E, F, G and H, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, E, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I, J, K and L, optionally additionally contains haplotype M; haplotypes C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes. C, E, F, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, F, G, H and L, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes C, D, G, H and L, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; and / or haplotypes B, C, D, E, G, I and L, optionally additionally containing haplotype M.

In some embodiments, an object of the invention disclosed herein also relates to hybrid or inbred Zea mays plants that have been modified to include a transgene. In some embodiments, a transgene encodes a gene product that provides resistance to a herbicide selected from glyphosate, sulfonylurea, imidazolinin, dicamba, glufisinate, phenoxypropionic acid, cycloshexome, triazine, benzonitrile, and broxinyl.

In some embodiments, an object of the invention disclosed herein also relates to methods for identifying Zea mays plants containing at least one allele associated with optimizing water consumption, as disclosed herein. In some embodiments of the invention, the methods comprise: (a) genotyping at least one Zea mays plant with at least one nucleic acid marker selected from SEQ ID NOS: 1-60 and 400; and (b) selecting at least one plant Zea mays containing an allele of at least one of at least one nucleic acid marker associated with optimizing water consumption.

In some embodiments of the invention, an object of the invention disclosed herein also relates to Zea mays plants obtained by introgression of the locus allele of interest associated with a sign of optimization of water consumption into the Zea mays germplasm. In some embodiments, the introgression comprises (a) breeding a Zea mays plant that contains an allele of a locus associated with a sign of optimizing water consumption, wherein the locus associated with a sign of optimizing water consumption contains a nucleotide sequence that is at least 90% identical to any of the sequences SEQ ID NOs: 1-117, 400, and 401; and (b) introgression of the allele of interest into the germplasm of Zea mays lacking this allele.

In some embodiments, an object of the invention disclosed herein also relates to methods for detecting and / or breeding a drought tolerant corn plant or germplasm. In some embodiments of the invention, the methods disclosed herein comprise detecting in a corn plant or germinal plasma the presence of a marker associated with increased drought tolerance, the marker being selected from the group consisting of:

nucleotide G at a position that corresponds to position 100 of the sequence SEQ ID NO: 2, trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, nucleotide A at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide T in position cat paradise corresponds to position 173 sequence SEQ ID NO: 57 and the nucleotide G at a position which corresponds to position 267 sequence SEQ ID NO: 60;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 562 of the sequence SEQ ID NO: 25, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at the position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A in position to which corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position which corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide G at a position that corresponds to position 100, nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 217 of SEQ ID NO: 23, nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide G at the position that corresponds to position 472 of the last successive SEQ ID NO: 48, a nucleotide G at a position which corresponds to position 193 sequence SEQ ID NO: 55 and the nucleotide C at a position which corresponds to position 486 sequence SEQ ID NO: 58;

a nucleotide deletion at a position that corresponds to positions 264-271 of SEQ ID NO: 2, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, and nucleotide C at the position that corresponds to position 486 of the sequence SEQ ID NO: 58;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 254 of the sequence SEQ ID NO: 27, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, nucleotide G at the position that corresponds to position 193 of the sequence SEQ ID N0: 55, nucleotide C in position cat the original corresponds to position 516 of the sequence SEQ ID NO: 56, nucleotide G at the position that corresponds to position 729 of the sequence SEQ ID NO: 59, and nucleotide G at the position that corresponds to position 267 of the sequence SEQ ID NO: 60;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55, and a nucleotide G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 472 of SEQ ID NO: 48, nucleotide A at a position that corresponds to position 237 of SEQ ID NO: 56, and nucleotide T at a position which corresponds to position 173 of the sequence SEQ ID NO: 57;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position that corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at the position that corresponds to position 87 of the sequence SEQ ID NO: 47, nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48, and a nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide A at a position that corresponds to position 309 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, and nucleotide G at a position which corresponds to position 193 of the sequence SEQ ID NO: 55;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7;

nucleotide A at a position that corresponds to position 4641 of the sequence of SEQ ID NO: 7;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, and nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, and nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48,

and combinations thereof, thereby detecting and / or selecting a drought tolerant corn plant or germplasm.

Thus, an object of the subject invention disclosed herein is to provide methods for transferring one or more signs of optimizing water consumption in corn germplasm.

The foregoing objective of the subject matter disclosed herein is, in whole or in part, achieved by the subject matter disclosed herein; other objectives will become apparent as they are further described, as best described below.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 is a graphical depiction of the alleles present in several loci of some varieties of corn used in the crossing protocols described herein.

Figure 2 is a graphical representation of the haplotypes of homozygous plant lines obtained from crossing NP2391 and CML333 ("homozygous CML333-" and "homozygous CML333 +") and hybrid lines F1 obtained from crossing each of the aforementioned homozygous lines NP2460 ("CML333-" H " CML333 + "). Alleles inherited from the CML322 donor line are indicated in lower case letters. Capital letters denote alleles inherited from NP2391 or NP2460.

Figure 3 is a graphical representation of the haplotypes of homozygous plant lines obtained from crossing NP2391 and CML322 ("homozygous CML322-" and "homozygous CML322 +") and F1 hybrid lines obtained from crossing each of the aforementioned homozygous lines NP2460 ("CML322- and" CML322 + "), Alleles inherited from the CML322 donor line are indicated in lowercase letters. Capital letters indicate alleles inherited by OTNP2391 or NP2460.

Figure 4 is a graphical representation of the haplotypes of homozygous plant lines obtained from crossing NP2391 and Cateto SP VII ("homozygous Cateto -" and "homozygous Cateto +") and F1 hybrid lines obtained from crossing each of the aforementioned homozygous lines NP2460 ("Cateto-" and "Cateto +"). Alleles inherited from the Cateto SP VII donor line are indicated in lower case letters. Capital letters indicate alleles inherited by OTNP2391 or NP2460.

Figure 5 is a graphical representation of haplotypes of homozygous plant lines obtained from crossing NP2391 and Confite Miliospo AYA 38 ("homozygous Confite -" and "homozygous Confite +") and F1 hybrid lines obtained from crossing each of the aforementioned homozygous NP2460 lines ("Confite- "and" Confite + "). The alleles inherited from the Confite Milyospo AYA 38 donor line are shown in lowercase letters. The alleles inherited from NP2391 or NP2460 are capitalized.

Figure 6 is a graphical representation of haplotypes of homozygous plant lines obtained from crossing NP2391 and Tuxpeno VEN 692 ("homozygous Tuxpeno-" and "homozygous Tuxpeno +") and F1 hybrid lines obtained from crossing each of the aforementioned homozygous NP2460 lines ("Tuxpeno- and "Tuxpeno +"). Lower case letters denote alleles inherited from the Tuxpeno VEN 692 donor line. Capital letters denote alleles inherited from NP2391 or NP2460.

For each of the figures 1-6, the alleles are as follows:

Allele Nucleotide Position and SEO ID NO: one Position 87 SEQ ID NO: 47 2 Position 386 SEQ ID NO: 46 3 Positions 4979-4981 SEQ ID NO: 7 four Position 4641 SEQ ID NO: 7 5 Position 472 SEQ ID NO: 48 6 Position 237 SEQ ID NO: 56 7 Position 516 SEQ ID NO: 56 8 Position 266 SEQ ID NO: 44 9 Position 475 SEQ ID NO: 45 10 Position 173 SEQ ID NO: 57 eleven Position 746 SEQ ID NO: 24 12 Position 391 SEQ ID NO: 33 13 Position 258 SEQ ID NO: 29 fourteen Position 217 SEQ ID NO: 23 fifteen Position 116 SEQ ID NO: 23 16 Position 463 SEQ ID NO: 19 17 Position 309 SEQ ID NO: 19 eighteen Positions 264-271 SEQ ID NO: 2 19 Position 100 SEQ ID NO: 2 twenty Position 486 SEQ ID NO: 58 21 Position 111 SEQ ID NO: 51 22 Position 254 SEQ ID NO: 27 23 Position 729 SEQ ID NO: 59 24 Position 267 SEQ ID NO: 60 25 Position 562 SEQ ID NO: 25 26 Position 1271 SEQ ID NO: 26 27 Position 193 SEQ ID NO: 55

BRIEF DESCRIPTION OF THE LIST OF SEQUENCES

The present disclosure contains many nucleotide and / or amino acid sequences. Throughout the disclosure and accompanying list of sequences, WIPO Standard ST.25 (1998, hereinafter referred to as “ST.25 Standard”) is used to identify nucleotides. This nucleotide identification standard is provided below.

table 2 Nucleotide Conventions in WIPO Standard ST.25 Symbol Value Symbol Value but but k g or t / u from from S g or c g g W a or t / u t t b g or c or t / u u u d a or g or t / u r g or a h a or c or t / u v t / u or s v a or g or c m a or c n a or g or c or t / u, unknown, other or absent

In some cases, the accompanying sequence listing includes one or more specific definitions for certain nucleotide positions, as set forth in lines <220> to <223> of the corresponding sequence listing entries. For example, while in accordance with ST.25 the nucleotide "n" usually replaces any of a, c, g or t, in the sequence SEQ ID NO: 2 it is noted that the sequence "rmnnnnnn" at nucleotide positions 264-271 is defined to represent either the presence or absence of the CACCAAGG nucleotide sequence. Similarly, in the sequence SEQ ID NO: 5, it is noted that the sequence "nnnn" at nucleotide positions 818-821 is defined so as to represent either the presence or absence of the nucleotide sequence "CGCG". Thus, while throughout the present description it is necessary to follow the standard ST.25, Statement s and the list of sequences, some of the sequences disclosed here are specific deviations from the standard ST.25 and are marked accordingly.

Additionally, regardless of whether this is specifically noted or not, for each reading of "n" in the sequence listing, it should be understood that any single "n" (including all or some n in the sequence of consecutive n) may represent a, c, g, t / u, unknown or other nucleotide or its absence. Thus, if the opposite is not specifically defined in the sequence listing, then in some embodiments, “n” may not represent a nucleotide. For example, the sequence of SEQ ID NO: 7 contains a series of 52 n between nucleotides 4549 and 4600, inclusive. It is understood that one or more data n may be absent, including, but not limited to, all 52 or any subset thereof.

SEQ ID NO: 1 is a nucleotide sequence that is linked to a Zmlga4 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 2 is a nucleotide sequence that is linked to a Zea mays water optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 3 is a nucleotide sequence that is linked to a ZmDr1 water consumption optimization locus, subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 4 is a nucleotide sequence that is linked to a ZmDrA water optimization locus encoding a voltage-dependent anion channel, subsequences of which can be amplified from chromosome 7 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in the table below four.

SEQ ID NO: 5 is a nucleotide sequence that is linked to a ZmDr2 water consumption optimization locus, the subsequences of which can be amplified from chromosome 2 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 6 is a nucleotide sequence that is linked to a ZmDr3 water consumption optimization locus, subsequences of which can be amplified from chromosome 2 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 7 is a nucleotide sequence that is linked to a ZmDr4 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 8 is a nucleotide sequence that is linked to a ZmMa3 water consumption optimization locus, the subsequences of which can be amplified from chromosome 2 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 9 is a nucleotide sequence that is linked to a ZmDr6 water consumption optimization locus, the subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as indicated in Table 4 below.

SEQ ID NO: 10 is a nucleotide sequence that is linked to a ZmBglcn water consumption optimization locus, the subsequences of which can be amplified from chromosome 3 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 11 is a nucleotide sequence that is linked to a locus of optimization of water consumption ZmLOC100276591, the subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as described below in table 4. SEQ ID NO: 12 and 13 are nucleotide sequences that are associated with the locus of optimizing water consumption of ZmDr7, the subsequences of which can be amplified from chromosome 1 of the Zea mays genome using the polymerase chain reaction with the amplification primers as shown below in Table 4.

SEQ ID NO: 14 is a nucleotide sequence that is linked to a ZmDr8 water consumption optimization locus, subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 15 is a nucleotide sequence that is linked to a locus for optimizing water consumption of ZmHsp70, the subsequences of which can be amplified from chromosome 1 of the Zea mays genome using a polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 16 is a nucleotide sequence that is linked to a ZmDr9 water consumption optimization locus, the subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as indicated in Table 4 below.

SEQ ID NO: 17-represents the nucleotide sequence that is associated with the locus of optimization of water consumption ZmDrB, subsequences of which can be amplified from the genome of Zea mays using the polymerase chain reaction with amplification primers, as described below in table 4.

SEQ ID NO: 18 is a nucleotide sequence that is linked to a ZmAdh1-1s water consumption optimization locus, the subsequences of which can be amplified from chromosome 1 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 19 is a nucleotide sequence that is linked to a ZmDr10 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 20 is a nucleotide sequence that is linked to a ZmDrC water consumption optimization locus, the subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 21 is a nucleotide sequence that is linked to a ZmDr5 water consumption optimization locus, the subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 22 is a nucleotide sequence that is linked to a ZmDrD water optimization locus encoding a subtilisin-chymotrypsin inhibitor 2, the subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as indicated in the table below. four.

SEQ ID NO: 23 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 24 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 25 is a nucleotide sequence that is linked to a water consumption optimization locus ZmDr12, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 26 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 27 is a nucleotide sequence that is linked to a ZmDrE water optimization locus encoding a legumin-like protein (cl2-1), subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers such as listed below in table 4.

SEQ ID NO: 28 is a nucleotide sequence that is linked to a ZmDrF water optimization locus encoding a putative cellulose synthase whose subsequences can be amplified from chromosome 9 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 29, is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 30 is a nucleotide sequence that is linked to a water consumption optimization locus ZmDhn2, the subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 31 is a nucleotide sequence that is linked to a ZmDr16 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 32 is a nucleotide sequence that is linked to a ZmDr17 water consumption optimization locus, the subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 33 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 34 is the nucleotide sequence that is associated with the locus of optimizing water consumption of ZmZCN6, the subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown below in table 4.

SEQ ID NO: 35 is a nucleotide sequence that is linked to a ZmDrG water consumption optimization locus, subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 36 is a nucleotide sequence that is associated with a locus of optimization of water consumption ZmDhn1, the subsequences of which can be amplified from chromosome 6 of the Zea mays genome using polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 37 is a nucleotide sequence that is linked to a ZmDrH water consumption optimization locus, the subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 38 is a nucleotide sequence that is linked to a ZmDrI water consumption optimization locus, the subsequences of which can be amplified from chromosome 3 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 39 is a nucleotide sequence that is linked to a ZmDrJ water optimization locus encoding mcm5 DNA replication factor, the subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in table 4 below .

SEQ ID NO: 40 is a nucleotide sequence that is linked to a locus for optimizing water consumption of ZmH2B1, the subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 41 is a nucleotide sequence that is associated with a ZmDr3 water consumption optimization locus, the subsequences of which can be amplified from chromosome 2 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 42 is a nucleotide sequence that is linked to a ZmDrK water consumption optimization locus encoding inorganic phosphatase, subsequences of which can be amplified from the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 43 is a nucleotide sequence that is linked to a ZmCat1 water consumption optimization locus, the subsequences of which can be amplified from chromosome 5 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NOs: 44 and 45 are nucleotide sequences that are linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 46 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 47 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 48 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 49 is a nucleotide sequence that is linked to a ZmRIC1 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NOs: 50 and 51 are nucleotide sequences that are linked to the ZmPK4 water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 52 is a nucleotide sequence that is linked to a Zpu1 water consumption optimization locus, the subsequences of which can be amplified from chromosome 2 of the Zea mays genome using a polymerase chain reaction with amplification primers, as described in table 4 below.

SEQ ID NO: 53 is a nucleotide sequence that is linked to a ZmDrL water consumption optimization locus, subsequences of which can be amplified from chromosome 9 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 54 is a nucleotide sequence that is linked to a ZmDrM optimization water locus encoding a hexose transporter, subsequences of which can be amplified from chromosome 7 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 55 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 56 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 57 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 58 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 59 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, the subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 60 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 8 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NO: 400 is a nucleotide sequence that is linked to a Zea mays water consumption optimization locus, subsequences of which can be amplified from chromosome 4 of the Zea mays genome using a polymerase chain reaction with amplification primers, as shown in Table 4 below.

SEQ ID NOs: 61-117 and 401 are the nucleotide sequences in the GenBank® database (available online at the National Center for Biotechnology Information (NCBI) of the US National Institutes of Health) that correspond (i.e., come from the same chromosomal locus in Zea mays) to the sequences of SEQ ID NO: 1-60 and 400. The relationships between the sequences of SEQ ID NO: 1-60 and 400 and 61-117 and 401 are shown below in table 3.

Table 3 The sequences in the GenBank® database corresponding to the sequences SEO ID NO: 1-60 and 400 SEQ ID NO: GENBANK® Access Number Corresponding nucleotides * SEQ ID NO of the corresponding nucleotides one AC214546.3 79631-80177 61 2 AC206432.3 76561-76072 62 3 AC218964.2 18179-18598 63 four AC198035.3 158268-157254 64 5 AC204020.3 180680-179781 65 6 AC206638.3 120959-121302 66 7 AC206220.1 197895-190521 67 8 AC213636.3 7053-6486 68 9 AC184130.4 28529-28053 69 10 AC186650.4 44576-75791 70 eleven AC214515.3 46309-46830 71 12, 13 AC211214.4 215368-214930 72 fourteen AC199476.4 103707-103339 73 fifteen AC213668.4 30778-29943 74 16 AC196196.4 76499-75481 75 17 AC214144.3 162815-162317 76 eighteen AC190915.3 6402-5517 77 19 AC209819.3 153562-152716 78 twenty AC187243.3 135331-136145 79 21 AC203390.3 86249-86674 80 22 AC195458.3 170810-171228 81 23 AC201782.4 26367-27234 82 24 AC218166.3 71588-72496 83 25 AC194405.3 40048-39222 84 26 AC213631.3 77810-79676 85 27 AC217937.3 111822-111263 86 28 AC211740.4 24016-14511 87 29th AC199040.3 88703-89626 88 thirty AC203943.3 104038-102899 89 31 AC210725.4 219394-219870 90 32 AC231410.4 60838-60463 91 33 AC195798.3 48792-47973 92 34 AC183820.4 23492-22810 93 35 AC214256.3 19884-20648 94 36 AC214345.3 27168-26399 95 37 AC198140.3 149518-149097 96 38 AC204009.3 60314-59762 97 39 AC205343.3 136853-136242 98 40 AC196429.3 5293-5956 99 41 AC206638.3 118845-119524 one hundred 42 AC191554.3 29279-28345 101 43 AC197489.3 40538-39734 102 44, 45 AC212232.3 61043-62624 103 46 AC187869.3 65344-64604 104 47 AC212049.4 47472-46845 105 48 AC194834.3 115968-117051 106 49 AC187038.3 139008-139936 107 50, 51 AC212049.4 54492-53643 108 52 AC202148.4 92457-93062 109 53 AC194911.4 42128-41419 110 54 AC195167.2 55324-56161 111 55 AC202530.4 20157-19337 112 56 AC218457.2 26390-27041 113 57 AC195989.4 114536-115181 114 58 AC207558.3 122483-121881 115 59 AC204398.3 137510-138350 116 60 AC211925.4 71848-71390 117 400 AC 196429.3 5293-5956 401 * The numbers in this column, going from the lowest to the highest, indicate that the entry in the GenBank® database corresponds to the nucleotide sequence from the same chain as in the corresponding sequence disclosed in SEQ ID NOs: 1-60 and 400. For of those records in which the numbers in this column go from the highest value to the lowest value, the nucleotide sequence disclosed in the GenBank® database record is the reverse complement of the nucleotide sequence corresponding to the sequence in the sequence SEQ ID NOs: 1-60 and 400.

The sequences of SEQ ID NOs: 61-117 and 401 were added to the GenBank® database by the Genome Sequencing Center, Washington University School of Medicine in St. Louis, Missouri, USA. As indicated in the annotations to these records in the database, the sequences were part of the efforts of The Maize Sequencing Consortium to sequence the Zea mays genome. Currently, sequencing efforts have not been completed, and various parts of the Zea mays genome remain unsequenced and / or sequences have not been ordered (or potentially, have been disordered) in the GenBank® database.

Table 4 lists the sequences of SEQ ID NO. for oligonucleotides that can be used to amplify Zea mays nucleic acids derived from loci that correspond to the sequences of SEQ ID NOS: 1-117, 400 and 401, and examples of amplicons produced in this way. Table 4 shows the position of the nucleotide in each sequence locus sequence SEQ ID NO 1-60 related to polymorphism (in some embodiments of the invention SNP), which is associated with a sign of optimization of water consumption, as well as the corresponding position of the nucleotide for polymorphism in each amplicon.

Table 4 SEO ID NO for oligonucleotides that can be used to amplify and / or analyze Zea mays loci corresponding to the sequences of SEO ID NO: 1-117, 400 and 401 Locus (SEQ ID NO) Examples of amplification primers (SEQ ID NO) SNP position (s) in the sequence of SEQ ID NO: 1-60 Examples used in the analysis of primers (SEQ ID NO) 1, 61 118 and 119 115 270 232, 233 301 483 2, 62 120 and 121 one hundred 348, 349 264-271 346, 347 3, 63 122 and 123 216 234, 235 4, 64 124 and 125 503 236, 237 5, 65 126 and 127 818-821 238, 239 6, 66 128 and 129 254 240, 241 7, 67 130 and 131 4497-4498 246, 247 4505 4609 4641 244, 245 352, 353 4792 248, 249 4836 250, 251 4844 4969 4979-4981 242, 243 350, 351 8, 68 132 and 133 217 252, 253 390 477 9, 69 134 and 135 292 254, 255 10, 70 136 and 137 166 256, 257 11, 71 138 and 139 148 258, 259 12, 13, 140 and 141 94 (12) 260, 261 72 35 (13) 262, 263 86 (13) 264,265 89 (13) 266, 267 14, 73 142 and 143 432 268, 269 15, 74 144 and 145 753 270, 271 16, 75 146 and 147 755 272, 273 17, 76 148 and 149 431 274, 275 18.77 150 and 151 518 276, 277 19, 78 152 and 153 182 280, 281 309 282, 283 356, 357 330 463 278, 279 354, 355 20, 79 154 and 155 773-776 284, 285 21.80 156 and 157 61 200 316-324 286, 287 22, 81 158 and 159 211 288, 289 23, 82 160 and 161 116 360, 361 217 358, 359 24, 83 162 and 163 746 362, 363 25, 84 164 and 165 562 290, 291 364, 365 26, 85 166 and 167 1271 366, 367 27, 86 168 and 169 64 254 292, 293 368, 369 28, 87 170 and 171 98 147 224 496 294, 295 29, 88 172 and 173 258 370, 371 30, 89 174 and 175 259 298, 299 296 398 296, 297 1057 31, 90 176 and 177 239 300, 301 32, 91 178 and 179 208 302, 303 33, 92 180 and 181 391 372, 373 34, 93 182 and 183 144-145 304,305 169 308, 309 537 306, 307 35, 94 184 and 185 76 310, 311 36, 95 186 and 187 500 568 698 312, 313 37, 96 188 and 189 375 316, 317 386 314, 315 38, 97 190 and 191 309 318, 319 342 320,321 39, 98 192 and 193 445 322, 323 40, 99 194 and 195 602 324, 325 41, 100 196 and 197 190 326, 327 580 328, 329 42, 101 198 and 199 238 266-268 330, 331 808 43, 102 200 and 201 708 332, 333 44, 45, 202 and 203 266 (44) 374, 375 103 475 (45) 376, 377 46, 104 204 and 205 386 378, 379 47, 105 206 and 207 87 380, 381 48, 106 208 and 209 472 382, 383 49, 107 210 and 211 166 24 650 334, 335 892 50, 51, 212 and 213 111 (51) 384, 385 108 541 (50) 336, 337 52, 109 214 and 215 442 338, 339 53, 110 216 and 217 83 428 342, 343 491 340, 341 548 54, 111 218 and 219 126 344, 345 55, 112 220 and 221 193 386, 387 56, 113 222 and 223 237 388, 389 516 390, 391 57, 114 224 and 225 173 392, 393 58, 115 226 and 227 486 394, 395 59, 116 228 and 229 729 396, 397 60, 117 230 and 231 267 398, 399 400, 401 402,403; 83 408, 409; 404, 405; 119 410, 411; 406, 407 601 412, 413

As can be seen from tables 3 and 4, some of the sequences of SEQ ID NO: 1-399 are linked to each other. For example, SEQ ID NO: 1 is the nucleotide sequence from Zea mays, which was mapped at the Zmlga4 locus on chromosome 8 of Zea mays. The subsequence of SEQ ID NO: 1 can be amplified in an amplification reaction (eg, PCR) to obtain an amplicon using oligonucleotides having the sequences of SEQ ID NO: 118 and 119 below. At position 270 of SEQ ID NO: 1, there is SNP and a specific nucleotide that is present in any nucleic acid sample at this position can be determined using oligonucleotides having the sequences of SEQ ID NO: 232 and 233 below.

In addition, the GenBank® accession number AC214546.3 includes a subsequence (e.g., nucleotides 79,631-80,177; sequence SEQ ID NO: 61), which itself is very similar to the sequence SEQ ID NO: 1 (with 538 identical nucleotides of 552 nucleotides, the percentage of identity is 98%) and, therefore, is present in the same locus from which the sequence SEQ ID NO is derived: 1. Differences between the two sequences (which can be detected using the BLAST algorithm, ClustalX algorithm, or any other suitable analysis method) t be attributed to normal variability within the Zea mays populations. The subsequence of SEQ ID NO: 61 can also be amplified in an amplification reaction (eg, PCR) to obtain an amplicon using oligonucleotides having the sequences SEQ ID NO: 118 and 119 below. Oligonucleotides having the sequences SEQ ID NO: 232 and 233 below can also be used to analyze the nucleotide base, which is in the position corresponding to position 270 of the sequence SEQ ID NO: 1.

For sequences SEQ ID NO: 2-399, similar relationships exist with the sequences described above, and one skilled in the art can identify them using conventional sequence analysis methods. It should be noted that for some of the sequences of SEQ ID NOs: 1-60, 400, the complete nucleotide sequence of the genomic clone, which includes the full-length sequence corresponding to these sequences, may not have been added by The Maize Sequencing Consortium to the GenBank database ®. However, using the sequence information disclosed herein, one skilled in the art can uniquely identify Zea mays loci that correspond to the sequences of SEQ ID NO: 1-117.

DETAILED DESCRIPTION OF THE INVENTION

An object of the invention disclosed herein relates to compositions and methods for detecting, breeding and / or producing maize with increased drought tolerance (also referred to here as water consumption optimization), as well as to maize plants identified, selected and / or produced by the method of the present invention. In addition, an object of the invention disclosed herein relates to corn plants and / or germplasm having in their genomes one or more markers associated with increased drought tolerance.

To evaluate the values of alleles and / or haplotypes during drought, various germplasm plasmas were screened in controlled field experiments containing a control treatment with full irrigation and an experimental treatment with limited irrigation. The purpose of full irrigation treatment was to ensure that water did not limit crop productivity. On the contrary, the purpose of limited irrigation processing was to ensure that water became the main limiting factor limiting grain yields. The main acting factors (for example, treatment and genotype) and their interactions (for example, genotype x treatment) can be detected when two types of treatment were used next to each other in this field. Moreover, drought-induced phenotype was quantified for each genotype in the panel, thereby allowing marker: trait associations.

In practice, the method of treatment with limited irrigation can vary widely depending on the germplasm being screened, the type of soil, the climatic conditions in place, the irrigation regime before the start of the season and the irrigation regime in season, etc. Initially, a place is determined where there is little rainfall during the season (to minimize the chance of unintentional irrigation), and which is suitable for cultivating crops. In addition, it may be important to determine the timing of stress exposure in order to ensure consistency of screening at a given site from year to year or from site to site. The intensity of the treatment or, in some cases, the desired yield loss as a result of processing with limited irrigation can also be taken into account. Selecting too light a processing intensity may not reveal genotypic variation. Choosing too heavy a processing rate can lead to too much experimental error. Once the timing of the stress exposure is determined and a description of the processing intensity is made, irrigation can be carried out in such a way as to meet these goals.

I. Definitions

While it is believed that the following terms are well understood by a person skilled in the art, the following definitions are provided to facilitate explanation of the subject matter disclosed herein.

It is understood that all technical and scientific terms used herein, unless otherwise defined below, have the same meaning as is commonly understood by one of ordinary skill in the art. References to methods used herein are intended to indicate methods as is commonly understood in the art, including variations of these methods or substitutions of equivalent methods that would be apparent to those skilled in the art. While the following terms are believed to be well understood by a person skilled in the art, the following definitions are provided to facilitate explanation of the subject matter disclosed herein.

Following a long-standing convention of patent law, the terms: the indefinite article "a", the indefinite article "an" and the definite article "the" refer to "one or more" when applied in this application, including in the claims. For example, the expression “marker” refers to one or more markers. Similarly, the expression “at least one,” as used herein to mean a subject, refers, for example, to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 , 40, 45, 50, 75, 100 or more to these subjects, including, but not limited to, integer numbers from 1 to 100 and greater than 100.

Unless otherwise indicated, it should be understood that all numbers expressing amounts of ingredients, reaction conditions, etc., used in the description and claims are modified in all cases by the term “about”. The term "about" when used herein, when it comes to a measurable quantity, such as mass amount, weight, time, volume, concentration or percentage, is intended to encompass changes constituting ± 20% in some embodiments of the invention, constituting ± 10%, in some embodiments, ± 5%, in some embodiments, ± 1%, in some embodiments, ± 0.5%, in some embodiments, and in some s embodiments ± 0,1% from the specified amount, as such changes correspond to implement the disclosed methods. Accordingly, unless otherwise indicated, the numerical parameters set forth in this description and the attached claims are approximate and may vary depending on the desired properties, which should be acquired disclosed in this document, the object of the invention.

The term “and / or” as used herein means and encompasses any possible combinations of one or more of the associated listed elements, as well as the absence of combinations thereof when interpreted as opposing (“or”).

As used herein, the term "allele" refers to a variant or alternative form of sequence at a genetic locus. In diploids, one allele at each locus is inherited by the descendant separately from each of the parents. Two alleles of a given locus present in a diploid organism occupy corresponding places on a pair of homologous chromosomes, although a person skilled in the art understands that alleles of any particular individual do not necessarily represent all alleles that are present in a given species.

The term “time interval between dusting and the sweeping phase of pistillate columns” (ASI), as used here, refers to the difference between when a plant begins to drop pollen (dusting) and when it begins to sweep the pistil columns (in females). Data is collected for each site. In some embodiments, the interval is expressed in days.

The term “associated with” as used herein refers to a recognizable and / or evaluated relationship between two entities. For example, the expression "associated with a sign of optimizing water consumption" refers to a trait, locus, gene, allele, marker, phenotype, etc. or their expression, the presence or absence of which can affect the degree, level and / or speed with which the plant of interest or part of it grows, which has a sign of optimizing water consumption. Thus, the marker is “associated with” the trait when it is associated with it and when the presence of the marker is an indicator of whether the desired trait or trait form occurs and / or to what extent the desired trait or trait form will occur in the plant / germplasm, containing the marker. Similarly, a marker is “associated with” an allele when it is associated with it and when the presence of the marker is an indicator of whether the allele is present in the plant / germplasm containing the marker. For example, a “marker associated with increased drought tolerance” refers to a marker whose presence or absence can be used to predict whether or not the plant phenotype will be drought tolerant.

As used herein, the terms “backcross” and “backcrossing” refer to a method by which a descendant plant is cross-crossed back and forth with one of its parents. In the backcrossing scheme, the “donor” parent refers to the parent plant with the desired gene or locus to be introgressed. The parent recipient (applied one or more times) or the recurrent parent (applied two or more times) refers to the parent plant in which the gene or locus is introgressed. For example, see Ragot, M. et al. Marker-assisted Backcrossing: A Practical Example, in TECHNIQUES ET UTILIZATIONS DES MARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); and Openshaw et al., Marker-assisted Selection in Backcross Breeding, in proceedings of the symposium "analysis of molecular marker data," pp. 41-43 (1994). The initial crossing gives the F1 generation. The term "BC1" refers to the second use of the recurrent parent, "BC2" refers to the third use of the recurrent parent, and so on. In some embodiments of the invention, backcross is repeated with an individual descendant of each subsequent backcross generation, which itself is reciprocally crossed with the same parental genotype.

A centimorganide (“cM”) is a unit of measure for the frequency of recombination. One CM is 1% of the probability that a marker at one genetic locus will be separated from a marker at the second locus due to crossing over in one generation.

As used herein, the term “chromosome” is used in the sense of a self-reproducing genetic structure recognized in the art in a cell nucleus containing cell DNA and having a linear set of genes in its nucleotide sequence. The Zea mays chromosome numbers described herein refer to chromosome numbers set forth in Perm et al., 2002, which is based on the nomenclature system adopted by the L'institut National da Ia Recherché Agronomique (INRA; Paris, France).

The term "consensus sequence" as used herein refers to a DNA sequence designed to identify nucleotide differences (eg, SNP and Indel polymorphisms) in alleles at a locus. The consensus sequence may be a DNA strand at a locus and defines the nucleotide (s) at one or more positions (for example, at one or more SNPs and / or at one or more Indel) at the locus. In some embodiments of the invention, a consensus sequence is used to develop oligonucleotides and probes for detecting polymorphisms at a locus.

The term “comprising”, which is synonymous with the word “comprising”, “comprising” or “characterized”, is an inclusive or open concept that does not exclude additional, implied elements and / or stages of the method. “Containing” is a term in the art that means that the named elements and / or steps are present, but that other elements and / or steps can be added and are still within the scope of the relevant subject matter.

The expression “consisting of” as used herein excludes any element, step or ingredient that is not specifically mentioned. For example, when the expression "consists of" appears in a claim, and not immediately after the preamble, it limits only the element set forth in this paragraph, other elements are not excluded from the claims as a whole.

The expression "consisting mainly of" as used herein limits the scope of the relevant description or claims to the indicated materials and / or stages, as well as to those materials and / or stages that do not substantially affect the main (s) and new (s) characteristic (s) of the disclosed and / or the claimed object. For example, an object of the invention disclosed herein relates, in some embodiments, to the introgression of favorable alleles and / or haplotypes into corn plants. One locus that contains some favorable alleles and / or haplotypes is represented by the sequence SEQ ID NO: 7, which includes nine (9) different polymorphisms set forth herein, with nine different favorable alleles. For any given introgression effort with respect to the genetic locus corresponding to the sequence of SEQ ID NO: 7, the method may “consist essentially of” introgressing the detected favorable allele selected from nine given polymorphic locations, which means that said favorable allele is the only favorable allele introgressed into the progeny genome. It should be noted, however, that additional polymorphic loci will also be introgressed into the genome, although the consequences of such introgression may be unknown or not of interest.

With respect to the terms “comprising,” “consisting essentially of,” and “consisting of,” when one of these three terms is used herein, the subject disclosed herein and the claimed subject matter may include the use of either of the other two terms. For example, an object of the invention disclosed herein relates, in certain embodiments, to oligonucleotide primers comprising any of the sequences SEQ ID NO: 118-399 and 402-413. It is understood that the subject matter disclosed herein thus also contains oligonucleotide primers, which in some embodiments of the invention consist essentially of any of the sequences SEQ ID NOS: 118-399 and 402-113, as well as oligonucleotide primers that are some embodiments of the invention consist of any of the sequences of SEQ ID NO: 118-399 and 402-113. Similarly, it is also clear that in some embodiments of the invention, the methods of the subject matter disclosed herein comprise the steps disclosed herein, in some embodiments of the invention, the methods of the subject disclosed herein comprise essentially the steps that are disclosed, and in some embodiments of carrying out the invention, the methods of the subject matter disclosed herein comprise the steps that are disclosed herein.

As used herein, the terms “crossing” or “crossed” refer to the fusion of gametes through pollination to produce offspring (eg, cells, seeds or plants). This term covers both sexual crosses (pollination of one plant by another) and self-hybridization (self-pollination, for example, when pollen and an egg come from the same plant). The term “cross” refers to the act of fusing gametes through pollination to produce offspring.

The terms “variety” and “variety” as used herein refer to a group of similar plants that can be distinguished from other varieties within the same species by structural and genetic characteristics and / or productivity.

The terms “desired allele” and “allele of interest” as used herein are used interchangeably to mean an allele associated with a desired trait. In some embodiments, the expression “desired allele” and / or “allele of interest” may be associated with an increase or decrease in a given trait or in a given trait, depending on the nature of the desired phenotype. In some embodiments, the expression “desired allele” and / or “allele of interest” may be associated with a change in morphology, color, etc.

The terms “drought tolerance” and “drought tolerant” as used herein refer to the ability of plants to tolerate drought and / or thrive in drought conditions. Applied to germplasm, these terms refer to the ability of a plant that sprouts from germplasm to tolerate drought and / or thrive in a drought environment. Typically, a plant or germplasm is designated as “drought tolerant” if it exhibits “increased drought tolerance”.

As used herein, the term “increased drought tolerance” refers to an improvement, increase, or increase in one or more phenotypes of optimized water consumption compared to one or more control plants (for example, one or both parents or a plant that does not have a marker associated with increased drought tolerance) . Examples of phenotypes for optimizing water consumption include, but are not limited to, grain yield at standard percent moisture (YGSMN), grain moisture at harvest time (GMSTP), grain weight per plot (GWTPN), yield yield percentage (PYREC), yield reduction (YRED), the time interval between dusting and the sweeping phase of pistillate columns (ASI) and the percentage of infertile plants (RV). Thus, a plant that exhibits a higher YGSMN than one or both of its parents, if each is grown under drought conditions, displays increased drought tolerance and can be designated as "drought tolerant".

As used herein, the terms “elite” and “elite line” refer to any line that is essentially homozygous and is the result of breeding and selection in order to achieve the desired agronomic performance.

As used herein, the term “gene” refers to a hereditary unit that includes a DNA sequence that occupies a specific place on the chromosome and contains genetic instructions for a specific trait or trait in the body.

A “genetic map” is a description of gene-linked relationships between loci on one or more chromosomes within a given species, usually shown in diagrammatic or tabular form. For each genetic map, distances between loci are measured by recombination frequencies between them. Recombination between loci can be detected using various markers. A genetic map is the product of a mapped population, the types of markers used, and the polymorphic potential of each marker between different populations. The order of the loci and the genetic distances between them may differ from one genetic map to another.

The expression “genetic marker” as used herein refers to a nucleic acid sequence (eg, a polymorphic nucleic acid sequence) that has been identified as being associated with a locus or allele of interest, and which indicates the presence or absence of a locus or allele of interest in a cell or body. Examples of genetic markers include, but are not limited to, genes, DNA or RNA derived sequences, promoters, any untranslated regions of a gene, miRNAs, siRNA, QTL, transgenes, mRNAs, dsRNAs, transcriptional profiles and methylation patterns.

As used herein, the term “genotype” refers to the genetic constitution of an individual (or group of individuals) at one or more genetic loci, as opposed to an observable and / or detectable and / or manifest trait (phenotype). The genotype is determined by the allele (s) and / or haplotype (s) of one or more known loci that the individual has inherited from his parents. The term genotype can be used to denote an individual’s genetic constitution at one locus, at several loci, or, more generally, the term genotype can be used to denote an individual’s genetic structure for all genes in his genome. Genotypes can be characterized indirectly, for example, using markers, and / or are characterized directly by sequencing of the nucleic acid sequence.

The term "germplasm" as used herein refers to the genetic material of an individual or from an individual (eg, plant), a group of individuals (eg, plant line, variety or family) or a clone derived from a line, variety, species or culture. Germplasm may be part of an organism or cell, or may be separated from the organism or cell. In general, germplasm provides genetic material with a specific molecular device that provides a physical basis for some or all of the hereditary qualities of an organism or cell culture. The term germplasm, as used herein, includes cells, seeds or tissues from which new plants can be grown, as well as parts of plants, such as leaves, stems, pollen or cells, from which a whole plant can be obtained by cultivation.

A “haplotype” is an individual’s genotype at a variety of genetic loci, that is, a combination of alleles. Typically, the genetic loci that define the haplotype are physically and genetically linked, that is, they are on the same segment of the chromosome. The term “haplotype” may refer to polymorphisms at a particular locus, such as a single marker locus, or to polymorphisms at several loci along a chromosome segment.

A “heterosis group” contains a set of genotypes that work well when crossed with genotypes from another heterosis group. Hallauer et al. Corn breeding, in corn and corn improvement p. 463-564 (1998). Inbred lines are divided into heterosis groups and within the heterosis group are further divided into families based on several criteria, such as a pedigree, associations based on molecular markers, as well as performance in hybrid combinations. Smith et al., Theor. Appl. Gen. 80: 833 (1990).

The term “heterozygous” as used herein refers to genetic status when different alleles are located at the corresponding loci on the homologous chromosomes. As used herein, the term “homozygous” refers to genetic status when identical alleles are located at the corresponding loci on the homologous chromosomes. It should be noted that both of these terms can refer to positions of single nucleotides, positions of several nucleotides, regardless of whether they are adjacent or not, or to whole loci on homologous chromosomes.

As used herein, the term “hybrid” refers to a seed and / or plant obtained by crossing at least two genetically heterogeneous parents.

The term “hybrid” as used herein, when used in the context of nucleic acids, refers to a double-stranded nucleic acid molecule or duplex formed by hydrogen bonds between complementary nucleotides. The terms “hybridize” and “annealing” refer to a method in which single strands of nucleic acid sequences form double helix segments via hydrogen bonds between complementary bases.

The term “Illumina® GoldenGate® Assay” as used herein refers to a high performance genotyping assay kit sold by Illumina Inc. San Diego, California, USA, with which you can get SNP-specific PCR products. This analysis is described in detail on the Illumina Inc. website. and in Fan et al., 2006.

The term "in close proximity" as used herein, when used to describe a nucleic acid molecule that hybridizes to a DNA containing a polymorphism, refers to a nucleic acid that hybridizes to a DNA sequence directly adjacent to the polymorphic position of the nucleotide base. For example, a nucleic acid molecule that can be used in a single nucleotide extension assay is "in close proximity" to polymorphism.

As used herein, the term “improved” and its grammatical variants refers to a plant or part thereof, its progeny or tissue cultures, which, due to the presence (or absence) of a specific allele associated with optimizing water consumption (such as, but not limited to, alleles associated with with water consumption optimization disclosed here) is characterized by a higher or lower level of trait associated with the optimization of water consumption, depending on whether a higher or lower level desirable for a specific purpose.

As used herein, the term "inbred" refers to a substantially homozygous plant or variety. The term may refer to a plant or variety that is substantially homozygous throughout the genome or which is substantially homozygous for a portion of the genome of particular interest.

As used herein, the term “INDEL” (also used to refer to “indel”) refers to an insertion or deletion in a pair of nucleotide sequences, wherein the first sequence may be designated as having an insertion relative to the second sequence or the second sequence may be designated as having a deletion relative to the first sequence.

As used herein, the term "informative fragment" refers to a nucleotide sequence containing a fragment of a larger nucleotide sequence, and this fragment allows the identification of one or more alleles within a larger nucleotide sequence. For example, an informative fragment of the nucleotide sequence of SEQ ID NO: 1 contains a fragment of the nucleotide sequence of SEQ ID NO: 1 and allows the identification of one or more alleles (for example, nucleotide G at position 115 of SEQ ID NO: 1, nucleotide A at the position corresponding to the position 270 of SEQ ID NO: I, nucleotide T at a position that corresponds to position 301 of SEQ ID NO: 1, and / or nucleotide A at a position that corresponds to position 483).

The term “interrogative position” as used herein means a physical position on a solid substrate that can be used in an analysis to obtain genotyping data for one or more predetermined genomic polymorphisms.

The terms “introgression,” “introgression,” and “introgressive,” as used herein, refer to both natural and artificial transmission of a desired allele or combination of desired alleles of a genetic locus or genetic loci from one genetic background to another. For example, the desired allele at the specified locus can be transmitted by at least one descendant through sexual crosses between two parents of the same species, where at least one of the parents has the desired allele in the genome. Alternatively, for example, allele transfer can occur by recombination between two donor genomes, for example, in a fused protoplast, where at least one of the donor protoplasts has the desired allele in the genome. The desired allele may be the selected allele of the marker, QTL, transgene or the like. The offspring containing the desired allele can be crossed back and forth with a line having the desired genetic background and selected by the desired allele, whereby the desired allele is fixed in the desired genetic background. For example, a marker associated with increased drought tolerance can be introgressed from a donor to a recurrent parent that is not drought resistant or only partially drought resistant. The resulting offspring can be cross-crossed and selected repeatedly until the descendant acquires the drought tolerance allele against the genetic background of the recurrent parent.

As used herein, the term “isolated” refers to a nucleotide sequence (eg, a genetic marker) free of sequences that typically flank one or both sides of the nucleotide sequence in the plant genome. Thus, the expression "isolated and purified genetic marker associated with the sign of optimization of water consumption in Zea mays," can mean, for example, a recombinant DNA molecule, provided that one of the nucleic acid sequences, which, usually flanking such a recombinant DNA molecule in the in vivo genome, deleted or absent. Thus, isolated nucleic acids include, without limitation, recombinant DNA that exists as a separate molecule (including, but not limited to, fragments of genomic DNA produced by PCR or restriction endonuclease processing), without flanking sequences present, as well as recombinant DNA that embedded in a vector, autonomously replicating plasmid or in the genomic DNA of a plant as part of a fusion nucleic acid molecule or fusion nucleic acid molecule.

As used herein, the term “linkage” refers to a phenomenon in which alleles on the same chromosome tend to be transmitted together more often than would be expected in a random transmission if their transmission was independent. Thus, it is said that two alleles on the same chromosome are “linked” when they are separated from each other in the next generation in some embodiments of the invention in less than 50% of cases, in some embodiments of the invention in less than 25% of cases in some embodiments of the invention in less than 20% of cases, in some embodiments of the invention in less than 15% of cases, in some embodiments of the invention in less than 10% of cases, in some embodiments of the invention in less than 9% of cases, in some embodiments of the invention in less than 8% of cases, in some embodiments of the invention in less than 7% of cases, in some embodiments of the invention in less than 6% of cases, in some embodiments of the invention in less than 5% of cases, in some embodiments the implementation of the invention in less than 4% of cases, in some embodiments of the invention in less than 3% of cases, in some embodiments of the invention in less than 2% of cases and in some embodiments of the invention in less than 1% of cases.

Thus, "linkage" usually implies and may also refer to physical proximity on the chromosome. Thus, two loci are linked, if they are within some embodiments of the invention 20 centimeters (cm), in some embodiments of the invention 15 cm, in some embodiments of the invention 12 cm, in some embodiments of the invention 10 cm, in some embodiments 9 cm, in some embodiments, 8 cm, in some embodiments 7 cm, in some embodiments 6 cm, in some embodiments 5 cm, toryh embodiments 4 cM, in some embodiments, 3 cM, in some embodiments, 2 cM, and in some embodiments 1 cm apart. Similarly, the yield locus of an object of the invention disclosed herein is linked to a marker (e.g., a genetic marker) if it is in some embodiments within 20, 15, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 cM marker.

Thus, the term “linkage” refers to the extent to which the locus of one marker is associated with the locus of another marker or another locus (eg, drought tolerance locus). The linkage relationship between the molecular marker and phenotype can be defined as “probability” or “predetermined probability”. Grip can be expressed as the desired limit or range. For example, in some embodiments of the invention, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM).

In some embodiments of the disclosed object of the invention, it is advisable to determine the limits of the adhesion range, for example, from about 10 cm to about 20 cm, from about 10 cm to about 30 cm, or about 10 cm to about 40 cm. The closer the marker is linked to the second locus, the better the indicator for the second locus, which becomes a marker. Thus, “closely linked loci,” such as the marker locus and the second locus, represent a recombination frequency between loci of about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3% or 2 % or less. In some embodiments, the corresponding loci display a recombination frequency of about 1% or less, for example, about 0.75%, 0.5%, 0.25% or less. We can also say that two loci located on the same chromosome and at such a distance that recombination between these two loci occurs with a frequency of less than about 10% (for example, about 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5% or 0.25% or less) are "proximal to" each other. Since one cM is the distance between two markers, which shows a recombination rate of 1%, any marker is closely linked (genetically and physically) to any other marker that is in close proximity, for example, at a distance of about 10 cM or less. Two closely linked markers on the same chromosome can be placed at a distance of about 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25 cm or less from each other friend.

As used herein, the term “linkage disequilibrium” refers to nonrandom segregation of genetic loci or characters (or both). In any case, linkage disequilibrium means that the corresponding loci are in sufficient physical proximity along the length of the chromosome, so that they are separated together with a more than random (i.e. nonrandom) frequency (in the case of jointly separating characters, the loci that cause the characters are in sufficient proximity to each other). Markers that exhibit linkage imbalance are considered linkage. The linked loci are shared together in more than 50% of cases, for example, from about 51% to about 100% of cases. In other words, two markers that are shared together have a recombination rate of less than 50% (and, by definition, are separated by less than 50 cM on the same chromosome). As used here, cohesion can take place between two markers or between a marker and a phenotype. The marker locus may be “associated with” (linked to) a trait, for example, drought tolerance. The degree of adhesion of a molecular marker to a phenotypic trait is measured, for example, as the statistical probability of joint segregation of a given molecular marker with a phenotype.

Adhesion imbalance is most often estimated by the value of r ² , which is calculated by the formula described by Hill and Robertson, Theor. Appl. Genet. 38: 226 (1968). When r ² is 1, there is a complete linkage disequilibrium between the two marker loci, meaning that the markers were not recombined and have the same allele frequency. Values of r ² above 1/3 show a fairly strong coupling disequilibrium, which is applicable for mapping. Ardlie et al., Nature Reviews Genetics 3: 299 (2002). Thus, the alleles are in linkage disequilibrium when the r ² values between pairwise marker loci are greater than or equal to about 0.33, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0.

The term “linkage equilibrium” as used herein describes a situation where two markers are separated independently, that is, randomly distributed among offspring. Markers that show linkage equilibrium are considered unlinked (regardless of whether or not they lie on the same chromosome). Thus, the expression “linkage disequilibrium” is defined as the change in the expected relative frequency of gamete types in the population of many individuals in the same generation, so that two or more loci act as genetically linked loci. If the frequency in the population of the allele S is x, the allele s is x ', the allele B is y, and the allele b is y', then the expected frequency of genotype SB is xy, that of genotype Sb is xy ', that of genotype sB is x'y and such the sb genotype equals x'y ', and any deviation from these frequencies is an example of disequilibrium.

The expression “linkage group” as used herein refers to all genes or genetic traits that are on the same chromosome. Those loci within the linkage group that are close enough to each other can show linkage in genetic crosses. Since the likelihood of a crossover increases with the physical distance between loci on the chromosome, loci whose positions within the linkage group are far away from each other may not show a noticeable linkage in direct genetic tests. The term “linking group” is mainly used to refer to genetic loci that exhibit linked behavior in genetic systems for which chromosome localization of genes has not yet been performed. Thus, in the present context, the term “linkage group” is synonymous with a chromosome as a physical subject, although one skilled in the art understands that a linkage group can also be defined as corresponding to a region (for example, smaller than the full chromosome) of a given chromosome.

A “locus” is a position on the chromosome where a gene or marker or allele is located. In some embodiments of the invention, the locus may comprise one or more nucleotides.

As used herein, the term "maize" means the plant Zea mays L. subspecies mays, also known as "corn."

As used herein, the term "corn plant" includes whole corn plants, corn plant cells, protoplast corn plants, a corn plant cell or corn tissue cultures from which corn plants, corn plant calluses and corn plant cells that are intact in corn can be regenerated plants, or parts of corn plants, such as corn seeds, corn cobs, corn flowers, corn cotyledons, corn leaves, corn stalks, corn buds, roots to kuruzy, the tips of the roots of the corn and the like.

The terms “marker”, “genetic marker”, and “molecular marker” as used herein are used interchangeably to indicate an identifiable position on a chromosome whose inheritance can be verified and / or a reagent that is used in methods for visualizing differences in nucleic acid sequences present in such identifiable positions on chromosomes. Thus, in some embodiments, the marker contains a known or detectable nucleic acid sequence. Examples of markers include, but are not limited to, genetic markers, protein composition, peptide levels, protein levels, oil composition, oil levels, carbohydrate composition, carbohydrate levels, fatty acid composition, fatty acid levels, amino acid composition, amino acid levels, biopolymers, starch composition, starch levels, fermentable starch, fermentation yield, fermentation efficiency (for example, defined as digestibility after 24, 48 and / or 72 hours), energy output, secondary substances, metabolites, morphological characteristics and agronomic characteristics. As such, the marker may contain a nucleotide sequence that has been associated with an allele or alleles of interest and indicates the presence or absence of an allele or alleles of interest in a cell or organism, and / or this nucleotide sequence is an indicator for a reagent that used to visualize differences in the nucleotide sequence in such an identifiable position or positions. A marker may include, but is not limited to, an allele, gene, haplotype, restriction fragment length polymorphism (RFLP), simple repeat sequences (SSR), randomly amplified polymorphic DNA (RAPD), split amplified polymorphic sequences (CAPS) (Rafalski and Tingey , Trends in Genetics 9: 275 (1993)), amplified fragment length polymorphism (AFLP) (Vos et al., Nucleic Acids Res. 23: 4407 (1995)), single nucleotide polymorphism (SNP) (Brookes, Gene 234: 177 ( 1993)), a known sequence amplified region (SCAR) (Paran and Michelmore, Theor. Appl. Ge net. 85: 985 (1993)), labeled sequence site (STS) (Onozaki et al., Euphytica 138: 255 (2004)), single-stranded DNA conformation polymorphism (SSCP) (Orita et al., Proc. Natl. Acad . Sci. USA 86: 2766 (1989)), sequences between simple repeat sequences (ISSR) (Blair et al., Theor. Appl. Genet. 98: 780 (1999)), polymorphic regions amplified between retrotransposons (IRAP), microsatellite polymorphic regions amplified between retrotransposons (REMAP) (Kalendar et al., Theor. Appl. Genet. 98: 704 (1999)), or an RNA cleavage product (such as Lynx tag). The marker may be present in genomic or expressed nucleic acids (e.g., EST). The term marker may also refer to nucleic acids used as probes or primers (for example, a pair of primers) for use in amplification, hybridization and / or detection of nucleic acid molecules in accordance with methods well known in the art. A large number of molecular markers of corn are known in the art and published or available from various sources, such as the Maize GDB Internet resource and the Arizona Genomics Institute Internet resource, run by the University of Arizona.

In some embodiments, the marker corresponds to an amplification product obtained by amplification of a Zea mays nucleic acid with one or more oligonucleotides, for example, polymerase chain reaction (PCR). As used herein, the expression "corresponds to an amplification product" in the context of a marker refers to a marker that has a nucleotide sequence that is the same amplification product (given the mutations introduced by the amplification reaction and / or natural and / or artificial allelic differences) as the product amplification obtained by amplification of Zea mays genomic DNA with a specific set of oligonucleotides. In some embodiments, the amplification is carried out by PCR, and the oligonucleotides are PCR primers that are designed to hybridize the opposite strands of Zea mays genomic DNA in order to amplify the Zea mays genomic DNA sequence present between sequences to which PCR primers hybridize to genomic DNA of Zea mays. The amplified fragment obtained from one or more amplification cycles using this arrangement of primers is a double stranded nucleic acid, one strand of which has a nucleotide sequence that contains in the direction from 5 'to 3' the sequence of one of the primers, the Zea mays genomic DNA sequence, located between the primers, and the sequence inverse complementary to the second primer. Typically, a “direct” primer is a primer that has the same sequence as the subsequence of the (randomly assigned) “upper” double stranded nucleic acid strand to be amplified, so that the “upper” strand of the amplified fragment includes a nucleotide sequence that in the direction from 5 'to 3' is equivalent to the sequence of the forward primer sequence located between the forward and reverse primers of the upper thread of the genomic fragment of the sequence, about complementary to the return primer. Thus, a marker that "matches" the amplified fragment is a marker that has the same sequence as one of the strands of the amplified fragment.

Markers corresponding to genetic polymorphisms between members of a population can be detected by methods well established in the art. These include, for example, nucleic acid sequencing, hybridization methods, amplification methods (for example, PCR-specific sequence amplification methods), detection of restriction fragment length polymorphisms (RFLP), detection of isoenzyme markers, detection of polynucleotide polymorphisms of allele-specific hybridization (ASH) , detection of amplified variable sequences of the plant genome, detection of self-replicating sequences, detection of simple repeats sequencing sequences (SSR), detecting a single nucleotide polymorphism (SNP) and / or detecting amplified fragment length polymorphism (AFLP) Well established methods are also known for determining expressed sequence labels (EST) and SSR markers derived from EST sequences and randomly amplified polymorphic DNA (RAPD).

A "marker allele", also described as a "marker locus allele," may refer to one of a plurality of polymorphic nucleotide sequences found at a marker locus in a population that is polymorphic to a marker locus.

The expression "marker analysis", as used here, refers to a method for determining polymorphism at a detected locus using a detected method, such as, but not limited to, measuring at least one phenotype (such as seed color, oil content or visually detectable trait) , nucleic acid-based assays, including but not limited to restriction fragment length polymorphism (RFLP), single nucleotide extension, electrophoresis, sequence alignment, allele-specific oligonuk leotide hybridization (ASO), random amplified polymorphic DNA analysis (RAPD), microarray technologies, TaqMan® assays, Illumina® GoldenGate® Assay assays, nucleic acid sequencing technologies, peptide and / or polypeptide assays, or any other method that may be used to determine polymorphism in the body at a locus of interest.

Marker selection (MAS) is a process in which phenotypes are selected based on marker genotypes.

"Counter-selection with markers" is a process in which marker genotypes are used to identify plants that will not be selected, which allows them to be removed from a breeding or planting program. As used herein, the terms “marker locus” and “marker loci” refer to a detected location or locations of a chromosome in an organism’s genome where a specific marker or markers can be found. A marker locus can be used to track the presence of a second linked locus, for example, a linked locus that encodes or promotes the expression of a phenotypic trait. For example, a marker locus can be used to monitor segregation of alleles at a locus, such as QTL or a single gene, that are genetically and physically linked to a marker locus.

As used herein, the terms “marker probe” and “probe” refer to a nucleotide sequence or nucleic acid molecule that can be used to detect the presence of one or more specific alleles at a marker locus (eg, a nucleic acid probe that is complementary to the entire marker or region thereof) or a marker locus via nucleic acid hybridization). Marker probes containing about 8, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more consecutive nucleotides can be used for nucleic acid hybridization. In addition, in some aspects of the invention, a marker probe refers to a probe of any type that is capable of distinguishing (i.e. genotyping) a specific allele that is present at a marker locus.

As used herein, the term "molecular marker" can be applied to a genetic marker, as defined above, or to an encoded product (eg, a protein) used as a "reference point" in identifying a linked locus. The molecular marker may be a derivative of genomic nucleotide sequences or expressed nucleotide sequences (e.g., from spliced RNA, cDNA, etc.). The term also refers to nucleotide sequences complementary to marker sequences or flanking marker sequences, such as nucleotide sequences used as probes and / or primers capable of amplifying marker sequences. Nucleotide sequences are "complementary" when they specifically hybridize in solution, for example, according to the Watson and Crick base pairing rules. Some of these markers described here are also called hybridization markers if they are in the INDEL region. This is because the insertion region is, by definition, a polymorphism with respect to the plant without insertion. Thus, the marker is only needed to indicate whether the INDEL region is present or absent. Any suitable marker identification technology may be used to identify such a hybridization marker, for example, the SNP technology is used in the examples provided herein.

The invention disclosed herein relates, in some embodiments, to markers for determining the presence of genetic polymorphisms at the corn loci described herein. Loci that can be analyzed using the compositions and methods of the subject disclosed herein include, but are not limited to, loci referred to herein as “ZmAdh1-s,” “ZmBglcn,” “ZmCat1,” “ZmDhn1” "," ZmDhn2 "," ZmDr1 "," ZmDr2 "," ZmDr3 "," ZmDr3 "," ZmDr4 "," ZmDr5 "," ZmDr6 "," ZmDr7 "," ZmDr8 "," ZmDr9 "," ZmDr10 " "ZmDr12", "ZmDr16", "ZmDr17", "ZmH2B1", "ZmHsp70", "Zmlga4", "ZmLOC100276591", "ZmMa3", "ZmPK4", "ZmRIC1", "ZmZCN6", "Zpu1" , "ZmDrB", "ZmDrC", "ZmDrD", "ZmDrE", "ZmDrF", "ZmDrG", "ZmDrH", "ZmDrI", "ZmDrj", "ZmDrk", "ZmDrL" and "ZmDr", names which, therefore, relate to genomic regions and / or genetic loci that are linked to traits associated with optimization of water consumption present on Zea mays chromosomes, and as described in more detail below Examples of genomic nucleotide sequences that originate from these loci are given above.

The term "ZmAdh1-1" refers to a locus on Zea mays chromosome 1 that encodes the alcohol dehydrogenase 1 gene (Dennis et al., 1984). Examples of gene products obtained from the ZmAdh1-1 locus can be found in GenBank® access numbers X04049 and P00333.

The term “ZmBglcn” refers to a locus on Zea mays chromosome 3 that encodes a maize 1,3-β-glucanase polypeptide (Wu et al., 1994). Examples of gene products derived from the ZmBglcn locus can be found in GenBank® access numbers M95407 and AAA74320.

The term "ZmCat1" refers to a locus on the Zea mays chromosome 5 that encodes a maize catalase-1 polypeptide (Guan & Scandalios, 1993). Examples of gene products derived from the ZmCat1 locus can be found in GenBank® access numbers X60135 and CAA42720.

The term "ZmDhn1" refers to a locus on the Zea mays chromosome 6 that encodes a maize dehydrin-1 (dhn1) polypeptide (Close et al., 1989). Examples of gene products derived from the ZmDhnI locus can be found in GenBank® access numbers X15290 and CAA33364.

The term "ZmDhn2" refers to a locus on chromosome 4 of Zea mays that encodes a maize dehydrin-2 (dhn2) polypeptide. Examples of gene products derived from the ZmDhn2 locus can be found in GenBank® access numbers L35913 and AA33480.

The term "ZmDr1" refers to the Zea mays locus, which in some embodiments corresponds to GenBank® Accession No. AY105200.

The term "ZmDr2" refers to the Zea mays locus, which in some embodiments of the invention corresponds to GenBank® Accession No AF043347.

The term "ZmDr3" refers to the Zea mays locus, which in some embodiments corresponds to nucleotides 120,959-121,302 from GenBank® Accession No. AC206638.3 and in certain embodiments corresponds to GenBank® Accession No. AF043347.

The term “ZmDr4” refers to the Zea mays locus, which in some embodiments corresponds to GenBank® Accession No. AY103545.

The term "ZmDr5" refers to the Zea mays locus, which in some embodiments corresponds to GenBank® Accession No. AY109606.

The term "ZmDr6" refers to the Zea mays locus, which encodes a corn calmodulin-binding protein. Examples of gene products obtained from the ZmDr6 locus can be found in GenBank® accession numbers L01497, NM_001158968, AAA33447 and NP_001152440.

The term "ZmDr7" refers to the Zea mays locus, which encodes a corn sucrose transporter protein. Examples of gene products derived from the ZmDr7 locus can be found in GenBank® accession numbers AB008464, NM_001111370, BAA83501. And NP_001104840.

The term "ZmDr8" refers to the Zea mays locus, which in some embodiments of the invention corresponds to GenBank® Accession No EU976286. The term "ZmDr9" refers to the Zea mays locus, which in some embodiments corresponds to nucleotides 75,481-76,499 of GenBank® Accession No AC 196196.4.

The term "ZmDr10" refers to the Zea mays locus, which in some embodiments of the invention corresponds to GenBank® Accession No. DQ245017.

The term "ZmDr12" refers to the Zea mays locus, which in some embodiments of the invention corresponds to GenBank® Accession No. AI770817.

The term "ZmDr16" refers to the Zea mays locus, which in some embodiments corresponds to GenBank® Accession No. NM_001156978.

The term "ZmDrl7" refers to the Zea mays locus, which in some embodiments corresponds to nucleotides 60,463-60,838 of GenBank® Accession No. AC231410.4.

The term "ZmDrA" refers to a locus on chromosome 7 of Zea mays, which encodes a voltage-dependent anion channel protein. An example of a gene product obtained from the ZmDrA locus can be found in GenBank® Accession No. BT018647.

The term "ZmDrB" refers to the Zea mays locus, which encodes a xylan endohydrolase protein. An example of a gene product obtained from the ZmDrB locus can be found in GenBank® Accession No. AI691894.

The term “ZmDrC” refers to the Zea mays locus that encodes a trehalose-P synthase protein. An example of a gene product obtained from the ZmDrC locus can be found in GenBank® Accession No. AY110270.

The term "ZmDrD" refers to a locus on the Zea mays chromosome 5 that encodes a subtilisin-chymotrypsin 2 inhibitor protein. An example of a gene product obtained from the ZmDrD locus can be found in GenBank® Accession No. BT066886.

The term "ZmDrE" refers to a locus on chromosome 8 of Zea mays that encodes a legumin-like protein (Cl2-1). Examples of gene products derived from the ZmDrE locus can be found in ® Accession Nos. NM_001111592 and NP_001105062.

The term "ZmDrF" refers to the locus on chromosome 9 of Zea mays, which encodes a protein of the putative cellulose synthase. Examples of gene products obtained from the ZmDrF locus can be found in GenBank® accession numbers BT067558 and ACN34455.

The term "ZmDrG" refers to a locus on chromosome 5 of Zea mays, which in some embodiments of the invention corresponds to GenBank® Accession No. AI691276.

The term "ZmDrH" refers to a locus on the Zea mays chromosome 5, which in some embodiments corresponds to GenBank® Accession No. AI665888.

The term "ZmDrI" refers to a locus on Zea mays chromosome 3, which in some embodiments corresponds to GenBank® Accession No. AI737958.

The term "ZmDrJ" refers to a locus on chromosome 5 of Zea mays that encodes the mcm5 DNA replication factor protein. Examples of gene products derived from the ZmDrJ locus can be found in GenBank® Accession No. AI666237.

The term "ZmDrK" refers to a Zea mays locus that encodes a pyrophosphatase protein, which in some embodiments corresponds to nucleotides 28,345-29,279 from GenBank® Accession No. AC191554.3.

The term "ZmDrL" refers to a locus on chromosome 9 of Zea mays, which encodes a protein similar to a protein of late embryonic development. An example of a gene product obtained from the ZmDrL locus can be found in GenBank® Accession No AY105938.

The term "ZmDrM" refers to a locus on the Zea mays 7 chromosome that encodes a hexose transporter protein. Examples of gene products obtained from the ZmDrM locus can be found in GenBank® access numbers NM_001154535 and NP_001148007.

The term "ZmH2B1" refers to a locus on chromosome 4 of Zea mays that encodes histone 2B1 of Zea mays. An example of a gene product obtained from the ZmDr6 locus can be found in GenBank® Accession No. AI737900.

The term “ZmHsp70” refers to the locus on Zea mays chromosome 1, which encodes a heat shock protein of maize related to the 70 kDa protein 2. Examples of gene products derived from the ZmDr7 locus can be found in GenBank® accession numbers EU971059, NM_001154726 and NP_001148198.

The term "Zmlga4" refers to a locus on chromosome 8 of Zea mays, which encodes a protein associated with the mutation liguleless4 (lg4). Examples of gene products obtained from the Zmlga4 locus can be found in GenBank® accession numbers AF457121, NM_001111614, AAM27190 and NP_001105084.

The term "ZmLOC100276591" refers to a locus that, in some embodiments, corresponds to GenBank® Access Numbers NM_001150343 and NP_001143815.

The term "ZmMa3" refers to a locus on Zea mays chromosome 2, which encodes a maize apoptosis ma-3 protein similar to topoisomerase. Examples of gene products obtained from the ZmMa3 locus can be found in GenBank® access numbers NM_001154442 and NP_001147914.

The term "ZmPK4" refers to the locus on chromosome 8 of Zea mays, which encodes the protein of the protein PK4 protein kinase. Examples of gene products originating from the ZmPK4 locus can be found in GenBank® accession numbers AF141378, NM_001111470, AAF22219 HNP_001104940.

The term "ZmRIC1" refers to a locus on the Zea mays chromosome 8, which encodes the maize protein RIC1, akin to the ras protein. Examples of gene products originating from the ZmRIC1 locus can be found in GenBank® accession numbers EU952511, NM_001137272, ACG24629 and NP_001130744.

The term "ZmZCN6" refers to a locus on the Zea mays 4 chromosome that encodes the corn protein ZCN6. Examples of gene products originating from the ZmZCN6 locus can be found in GenBank® accession numbers EU241897, NM_001112774, ABX11008 and NP_001106245.

The term "Zpu1" refers to a locus on the Zea mays 2 chromosome that encodes a protein zpu1 enzyme that hydrolyzes starch by the pullulanase type. Examples of gene products obtained from the Zpu1 locus can be found in GenBank® accession numbers AF080567, NM_001111450, AAD11599 and NP_001104920.

As used herein, the expression “native trait” refers to any existing monogenic or oligogenic trait in the germplasm of certain cultures. When identified through molecular (e) marker (s), the information obtained can be used to improve germplasm by crossing using markers associated with the optimization of water consumption characteristics disclosed herein.

A "non-naturally occurring corn variety" is any corn variety that does not naturally exist in nature. A "non-naturally occurring corn variety" can be obtained by any method known in the art, including, but not limited to, transforming corn or germplasm, transfecting corn or germplasm, and crossing a natural corn variety with a non-naturally occurring corn variety . In some embodiments, an “unnatural corn variety” may contain one or more heterologous nucleotide sequences. In some embodiments, a “non-naturally occurring maize variety” may contain one or more non-naturally occurring copies of a natural nucleotide sequence (eg, extraneous copies of a gene that is found in maize under natural conditions).

The heterosis group "Non-Stiff Stalk" is a large heterosis group in the corn growing regions of the northern United States and Canada. It can also be called the heterotic group "Lancaster" or "Lancaster Sure Crop".

As used herein, the terms “nucleotide sequence”, “polynucleotide”, “nucleic acid sequence”, “nucleic acid molecule” and “nucleic acid fragment” refer to an RNA or DNA polymer that is single or double stranded, optionally containing synthetic, unnatural and / or altered nucleotide bases. A "nucleotide" is a monomer unit from which polymers of DNA or RNA are constructed, and consists of a purine or pyrimidine base, pentose and a phosphoric acid residue. Nucleotides (usually found in the form of 5'-monophosphate) are named according to their single-letter designations as follows: “A” for adenylate or deoxyadenylate (for RNA or DNA, respectively), “C” for citidylate or deoxycytidylate, “G” for guanylate or deoxyguanilate , “U” for uridylate, “T” for deoxythymidylate, “R” for purines (A or G), “Y” for pyrimidines (C or T), “K” for G or T, “H” for A or C or T, “I” for inosine and “N” for any nucleotide.

As used herein, the term "nucleotide sequence identity" means the presence of identical nucleotides at the corresponding positions of two polynucleotides. Polynucleotides have "identical" sequences if the nucleotide sequence in the two polynucleotides is the same when aligned for maximum match (for example, in the comparison window). Comparison of the sequence between two or more polynucleotides is usually performed by comparing portions of two sequences throughout the comparison window to identify and compare local regions of similarity of the sequence. The comparison window typically ranges from 20 to 200 consecutive nucleotides. The “percent sequence identity” for polynucleotides, such as 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 98, 99, or 100 percent sequence identity, can be determined by comparing two optimally aligned sequences throughout the comparison window wherein the portion of the polynucleotide sequence in the comparison window may include additions or deletions (eg, spaces), compared with the reference sequence, for optimal alignment of the two sequences. The percentage is calculated: (a) by determining the number of positions in which an identical nucleic acid base is found in both sequences, (b) dividing the number of corresponding positions by the total number of positions in the comparison window, and (c) multiplying the result by 100. Optimal alignment of sequences for comparison can be carry out using computerized implementations of known algorithms or by viewing. Easily accessible algorithms for comparing sequences and multiple sequence alignment are, respectively. Basic Local Alignment Search Tool (BLAST) and ClustalW, available on the Internet. Other suitable programs include, but are not limited to, GAP, BestFit, Plot Similarity, and FASTA, which are part of the Accelrys GCG package available from Accelrys, Inc. of San Diego, California, USA. In some embodiments, the percent sequence identity indicates sequence identity over the entire length of one of the compared sequences. In some embodiments, the calculation of determining the percent sequence identity does not include any nucleotide positions in which one of the compared nucleic acids contains “N” (that is, when any nucleotide may be present at that position).

As used herein, the term “percentage of infertile plants” (PB) refers to the percentage of plants in the discovered area (eg, plot) without grain. This concept is usually expressed in terms of the percentage of plants per plot and can be calculated as:

$$\frac{\mathrm{to}\mathrm{about}l\mathrm{and}he\mathrm{from}t\mathrm{at}\mathrm{about}R\mathrm{but}\mathrm{from}ten\mathrm{and}\mathrm{th}n\mathrm{but}\mathrm{at}h\mathrm{but}\mathrm{from}t\mathrm{to}ebesseRn\mathrm{but}}{\mathrm{about}buee\mathrm{to}\mathrm{about}l\mathrm{and}he\mathrm{from}t\mathrm{at}\mathrm{about}R\mathrm{but}\mathrm{from}ten\mathrm{and}\mathrm{th}n\mathrm{but}\mathrm{at}h\mathrm{but}\mathrm{from}t\mathrm{to}e}\times \mathrm{one\; hundred}$$

The term "yield yield" (PYREC) as used herein reflects the effect of alleles and / or a combination of alleles on the yield of a plant grown under drought conditions compared to that of a plant that is genetically identical, except that it lacks an allele and / or combinations of alleles. PYREC is calculated as:

$$\mathrm{one}-\frac{\begin{array}{l}\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tbPR\mathrm{and}P\mathrm{about}ln\mathrm{about}m\mathrm{about}R\mathrm{about}wen\mathrm{and}\mathrm{and}\left(\mathrm{from}\mathrm{and}nteRe\mathrm{from}\mathrm{at}\mathrm{Yu}ue\mathrm{th}(\mathrm{and}m\mathrm{and})\mathrm{but}llelb\mathrm{Yu}(\mathrm{I\; am}m\mathrm{and})\right)-\\ \mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xs\mathrm{but}\mathrm{from}\mathrm{at}x\mathrm{and}\left(\mathrm{from}\mathrm{and}nteRe\mathrm{from}\mathrm{at}\mathrm{Yu}ue\mathrm{th}(\mathrm{and}m\mathrm{and})\mathrm{but}llelb\mathrm{Yu}(\mathrm{I\; am}m\mathrm{and})\right)\end{array}}{\begin{array}{l}\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tbPR\mathrm{and}P\mathrm{about}ln\mathrm{about}m\mathrm{about}R\mathrm{about}wen\mathrm{and}\mathrm{and}(bes\mathrm{and}nteRe\mathrm{from}\mathrm{at}\mathrm{Yu}ue\mathrm{th}(\mathrm{and}x)\mathrm{but}llel\mathrm{and}(e\mathrm{th})-\\ \mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xs\mathrm{but}\mathrm{from}\mathrm{at}x\mathrm{and}(bes\mathrm{and}nteRe\mathrm{from}\mathrm{at}\mathrm{Yu}ue\mathrm{th}(\mathrm{and}x)\mathrm{but}llel\mathrm{and}(e\mathrm{th})\end{array}}\times \mathrm{one\; hundred}$$

By way of example, and not limitation, if a control plant produces 200 bushels under full irrigation, but only 100 bushels under drought, then its yield loss percentage will be calculated to be 50%. If another genetically identical hybrid that contains the allele (s) of interest produces 125 bushels in drought conditions and 200 bushels in full irrigation conditions, then the percent yield loss will be calculated to be 37.5%, and PYREC will be calculated as 25% [ 1.00- (200-125) / (200-100) × 100)].

The expression "grain yield - good irrigation" as used herein refers to a crop from an area with sufficient irrigation to prevent water deficiency in plants during the growth cycle. In some embodiments, the trait is expressed in bushels per acre.

The expression “yield reduction - hybrid” as used herein refers to a calculated trait derived from a study of the yield of a hybrid grown under stress and without stress. For this hybrid, this characteristic is equal to:

$$\frac{\begin{array}{l}\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}-\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\\ \mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}x\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}\end{array}}{\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}}\times \mathrm{one\; hundred.}$$

In some embodiments, the trait is expressed as a percentage of bushels per acre.

The expression “yield reduction - inbred” as used herein refers to a calculated trait derived from a study of the yield of an inbred that has grown under stress and without stress. For this inbred, this trait is equal to:

$$\frac{\begin{array}{l}\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}-\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\\ \mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}x\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}\end{array}}{\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}}\times \mathrm{one\; hundred.}$$

In some embodiments, the trait is expressed as a percentage of bushels per acre.

The term “time interval between dusting and the sweeping phase of pistillar columns” (ASI) as used herein refers to the difference (in some embodiments, expressed in days) between when a plant begins to dump pollen (dusting) and when it begins to sweep the pistillation season columns (females). Data on dusting and sweeping of pistillate columns are collected per site, and the difference is calculated.

The expression “percentage of infertile plants” as used herein refers to the percentage of plants in a given area (plot) without grain. It is usually expressed in terms of the percentage of plants on the site and can be calculated as:

$$\frac{\mathrm{to}\mathrm{about}l\mathrm{and}he\mathrm{from}t\mathrm{at}\mathrm{about}R\mathrm{but}\mathrm{from}ten\mathrm{and}\mathrm{th}n\mathrm{but}\mathrm{at}h\mathrm{but}\mathrm{from}t\mathrm{to}ebesseRn\mathrm{but}}{\mathrm{about}buee\mathrm{to}\mathrm{about}l\mathrm{and}he\mathrm{from}t\mathrm{at}\mathrm{about}R\mathrm{but}\mathrm{from}ten\mathrm{and}\mathrm{th}n\mathrm{but}\mathrm{at}h\mathrm{but}\mathrm{from}t\mathrm{to}e}\times \mathrm{one\; hundred.}$$

The terms “phenotype”, “phenotypic trait” or “trait”, as used herein, refer to one or more traits of an organism. The phenotype can be observed with the naked eye or by any other assessment method known in the art, for example, microscopy, biochemical analysis, or electromechanical analysis. In some cases, the phenotype is directly controlled by a single gene or genetic locus, that is, it is a “homogeneous trait”. In other cases, the phenotype is the result of several genes. It should be noted that, as used here, the term “phenotype of water consumption optimization” takes into account environmental conditions that may affect the optimization of water consumption, so that the effect of optimizing water consumption is real and reproducible.

As used herein, the term “plant” can refer to a whole plant, any part thereof, or to a cell or tissue culture derived from a plant. Thus, the term “plant” can refer to any of: whole plants, components or organs of a plant (eg leaves, stems, roots, etc.), plant tissues, seeds and / or plant cells.

A plant cell is a plant cell taken from a plant or originating through culture from a cell taken from a plant. Thus, the term “plant cell” includes, without limitation, cells in seeds, suspension cultures, embryos, meristematic regions, callus tissues, leaves, shoots, gametophytes, sporophytes, pollen and microspores. The term “plant part” refers to a part of a plant, including single cells and cell tissues, such as plant cells that are intact in plants, cell accumulations and tissue cultures from which plants can be regenerated. Examples of plant parts include, but are not limited to, individual cells and tissues from pollen, eggs, leaves, embryos, roots, root tips, anthers, flowers, fruits, stems, shoots and seeds, as well as cuttings, rhizomes, protoplasts, calluses and the like.

As used herein, the term “polymorphism” means a change in a nucleotide sequence at a locus where the change is too often to be associated simply with a spontaneous mutation. Polymorphism should have a frequency of at least about 1% in a population. The polymorphism may be a single nucleotide polymorphism (SNP) or an insertion / deletion polymorphism, also known here as "indel". Additionally, the change may take place in the transcription profile or methylation pattern. A polymorphic site or sites of a nucleotide sequence can be determined by comparing nucleotide sequences at one or more loci in two or more germplasm elements.

As used herein, the term “population” refers to a genetically heterogeneous collection of plants having a common genetic origin.

As used herein, the term “primer” refers to an oligonucleotide that is capable of annealing with a target nucleic acid (in some embodiments, specific annealing with a target nucleic acid), which allows DNA polymerase to attach, thereby serving as an initiation point for DNA synthesis under conditions which induces the synthesis of a primer extension product (for example, in the presence of nucleotides and a polymerization agent, such as DNA polymerase, and at a suitable temperature and pH). In some embodiments, a variety of primers are used to amplify Zea mays nucleic acids (eg, by polymerase chain reaction, PCR).

As used herein, the term “probe” refers to a nucleic acid (for example, a single-stranded nucleic acid or a double-stranded or higher-order nucleic acid strand or a subsequence thereof) that can form a hydrogen duplex with a complementary sequence in the target nucleic acid sequence. Typically, the probe is long enough to form with its complement a stable, sequence-specific duplex molecule, and as such may be used in some embodiments of the invention to determine the sequence of interest present in a large number of nucleic acids.

As used herein, the terms “offspring” and “plant-offspring” refer to a plant obtained by vegetative or sexual reproduction from one or more parent plants. A descendant plant can be obtained by cloning or self-pollination of one parent plant or by crossing two parent plants. Thus, the expression "plant-offspring" means any plant obtained as a progeny from plant or sexual reproduction from one or more parent plants, or its descendants. For example, a descendant plant can be obtained by cloning or self-pollination of a parent plant or by crossing two parent plants and includes selfies, as well as F1 or F2, as well as next generations. F1 is the first generation offspring obtained from parents, at least one of which is used for the first time as a character donor, while the second generation offspring (F2) or subsequent generations (F3, F4 and the like) are samples, obtained from self-pollination, cross-crossings, backcrosses or other crosses of generations F1, F2 and the like. F1 may thus be (and in some embodiments is) a hybrid resulting from a cross between two parents belonging to a clean line (for example, each parent who belongs to a clean line is homozygous for the trait of interest or its alleles), while F2 may be (and in some embodiments of the invention is) a descendant resulting from self-pollination of F1 hybrids.

The expression “quantitative trait locus” (QTL; quantitative trait loci — QTL) as used herein refers to a genetic locus (or loci) that control, to one degree or another, a quantitative trait, which in some embodiments of the invention is characterized by continuous distribution. In some embodiments, the QTL comprises a locus associated with optimizing water consumption. The expression "locus associated with water consumption optimization" as used herein is used to denote a chromosomal region containing alleles (for example, in the form of genes or regulatory sequences) associated with the expression of a trait associated with water consumption optimization. Thus, the locus "associated with" a sign of optimizing water consumption refers to one or more regions located on one or more chromosomes, which includes at least one gene, the expression of which affects the optimization of water consumption and / or at least one a regulatory region that controls the expression of one or more genes involved in one or more traits of optimizing water consumption. Loci can be determined by indicating their genetic location in the genome of a given Zea mays plant using one or more molecular genomic markers. One or more markers, in turn, indicate a specific locus. Distances between loci are usually measured by the crossover frequency between loci on the same chromosome. The farther two loci are located from each other, the greater the likelihood that a crossover will occur between them. On the other hand, if two loci are close to each other, it is less likely that a crossover will occur between them. Typically, one centimorganide (cM) equals 1% recombination between loci. When QTL can be identified by several markers, the genetic distance between the extreme markers indicates the size of the QTL.

The term "recombination" as used herein means the exchange of DNA fragments between two DNA molecules or chromatid paired chromosomes ("crossover") within the region of homologous or identical nucleotide sequences. A “recombination event" is understood here to mean a meiotic crossover.

The term "reference sequence" as used herein refers to a specific nucleotide sequence used as the basis for comparing nucleotide sequences. For example, a reference sequence for a marker is obtained by genotyping the number of lines at a locus or loci of interest, aligning nucleotide sequences with a sequence alignment program, and then obtaining a consensus sequence from alignment. Thus, the reference sequence reveals allele polymorphisms at the locus. The reference sequence may not be a copy of the actual nucleic acid sequence from any particular organism, however, this sequence is applicable for designing primers and probes for actual polymorphisms at a locus or loci.

As used herein, the term “regenerate” and its grammatical variations refer to the production of a plant from tissue culture.

The terms “selected allele”, “desired allele” and “allele of interest” as used herein are used interchangeably to refer to a nucleic acid sequence that includes a polymorphic allele associated with a desired trait. It should be noted that the “selected allele”, “the desired allele” and / or the “allele of interest” can be associated with both an increase in the desired trait and a decrease in the desired trait, depending on the nature of the phenotype that is sought in the introgressed the plant.

The term “single nucleotide polymorphism” or “SNP” as used herein refers to polymorphism, which is a one base pair difference between two nucleotide sequences. The term "SNP" as used herein also refers to differences between two nucleotide sequences that result from simple changes in one sequence relative to another occurring at one site in the sequence. For example, the term “SNP” is intended to mean not only sequences that differ by one nucleotide as a result of replacing one sequence in a nucleic acid compared to another, but also is intended to refer to sequences that differ by one, two, three or more nucleotides as a result of a deletion 1, 2, 3 or more nucleotides in one site of one of the sequences compared to another. It is clear that in the case of two sequences that differ from each other only by deletion of the 1st, 2nd, 3rd or more nucleotides in one site in one of the sequences compared to the other, the same scenario can be considered as adding 1, 2, 3 or more nucleotides in one site of one of the sequences compared to the other, depending on which of the two sequences is considered a reference sequence. Thus, it is believed that insertions and / or deletions in one site are also covered by the term “SNP”.

The Stiff Stalk heterosis group is a large heterosis group in the corn regions of the northern United States and Canada. It can also be called the heterosexual group "Iowa Stiff Stalk Synthetic" or "BSSS".

The term “stringent hybridization conditions” as used herein refers to conditions under which a polynucleotide hybridizes with its target sequence, typically in a complex mixture of nucleic acids, but with no other sequences. Strict conditions are sequence dependent and may vary in different circumstances.

Longer sequences usually hybridize specifically at higher temperatures. An extensive guide to nucleic acid hybridization can be found in Tijssen, 1993. In general, stringent hybridization conditions are chosen so that they are approximately 5-10 ° C below the melting temperature (Tm) of the specific sequence at a specific ionic strength and pH. Tm is the temperature (for a given ionic strength, pH, and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize under equilibrium conditions with the target sequence (since at Tm the target sequences are present in excess, then at equilibrium conditions 50 % probes). An example of stringent conditions are those under which the salt concentration is less than about 1.0 M sodium ions, typically about 0.01 to 1.0 M sodium ions (or other salts) at a pH of 7.0 to 8, 3 and a temperature of at least about 30 ° C for short probes (for example, containing from 10 to about 50 nucleotides) and at least about 60 ° C for long probes (for example, containing more than 50 nucleotides).

Strict conditions can also be ensured by the addition of destabilizing agents, such as formamide. An additional example of stringent hybridization conditions includes incubation in a buffer containing 50% formamide, 5 × SSC and 1% SDS at 42 ° C, or SSC, 1% SDS, with incubation at 65 ° C, with one or more washing with a mixture of 0 , 2 × SSC and 0.1% SDS at 65 ° C. In the case of PCR, a temperature of about 36 ° C is typical for amplification under low stringency conditions, although annealing temperatures can vary between about 32 ° C and 48 ° C (or higher), depending on the length of the primer. Additional instructions for determining hybridization parameters are provided in numerous references (see, for example, Ausubel et al., 1999).

The term “TaqMan® analysis” as used herein refers to real-time sequence detection by PCR based on the TaqMan® analysis kit sold by Applied Biosystems, Inc. of Foster City California, USA. For an identifiable marker, TaqMan® analysis can be debugged for use in a breeding program.

As used herein, the term “tester” refers to a line used in a test cross with one or more other lines, the test tester and line (s) being tested are genetically heterogeneous. The tester can be an isogenic line to a crossed line.

As used herein, the term “trait” refers to a phenotype of interest, a gene that contributes to a phenotype of interest, and a nucleic acid sequence associated with a gene that contributes to a phenotype of interest. For example, a "sign of water consumption optimization" refers to the phenotype of water consumption optimization, as well as to a gene that contributes to the phenotype of water consumption optimization and to the nucleic acid sequence (eg, SNP or other marker) that is associated with the phenotype of water consumption optimization.

The term "transgene" as used herein refers to a nucleic acid molecule introduced into the body or its ancestors by some form of artificial transfer method. The artificial transfer method thus creates a “transgenic organism” or “transgenic cell”. It is understood that the artificial transfer method can be carried out in an ancestor's body (or in a cell in it and / or in a cell that can develop into an ancestor's body), and yet any descendant individual that has an artificially transferred nucleic acid molecule or a fragment thereof is still considered transgenic, even if the presence of an artificially transferred nucleic acid molecule in a descendant individual is the result of one or more natural and / or forced dilutions.

An “unfavorable allele” of a marker is a marker allele that segregates with an unfavorable plant phenotype, thereby making it possible to identify plants that may be removed from a breeding or planting program. As used herein, the term "optimization of water consumption" means any parameter of a plant, its parts or its structure that can be measured and / or quantified in order to assess the degree and rate of growth and development of plants in conditions of sufficient presence of water compared to conditions of non-optimal presence of water (e.g. drought). As such, a "sign of optimizing water consumption" is any sign that, as can be shown, affects the yield of a plant under various combinations of growing conditions associated with the availability of water.

Similarly, "water consumption optimization" can be considered as a "phenotype", which, as used here, refers to a detectable, observable and / or measurable characteristic trait of a cell or organism. In some embodiments of the invention, the phenotype is based, at least in part, on the genetic composition of the cell or organism (hereinafter referred to as the "genotype" of the cell or organism). Examples of phenotypes for optimizing water consumption are grain yield at standard percent moisture (YGSMN), grain moisture at harvest time (GMSTP), grain weight per plot (GWTPN), yield yield percentage (PYREC). It should be noted that, as used here, the term “phenotype” takes into account how the environment (for example, environmental conditions) can affect the optimization of water consumption, so that the effect of optimizing water consumption is real and reproducible. As used herein, the term “yield reduction” (YD) refers to the extent to which yield decreases in plants grown under stress. YD is calculated by the formula:

$$\frac{\begin{array}{l}\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}-\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\\ \mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}x\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}\end{array}}{\mathrm{at}R\mathrm{about}\mathrm{well}\mathrm{but}\mathrm{th}n\mathrm{about}\mathrm{from}tb\mathrm{at}\mathrm{at}\mathrm{from}l\mathrm{about}\mathrm{at}\mathrm{and}\mathrm{I\; am}xbes\mathrm{from}tRe\mathrm{from}\mathrm{from}\mathrm{but}}\times \mathrm{one\; hundred}$$

II. Molecular Markers, Loci Associated with Water Consumption Optimization, and Compositions for Analyzing Nucleic Acid Sequences

Molecular markers are used to visualize differences in nucleic acid sequences. This visualization may be due to DNA-DNA hybridization techniques after digestion with a restriction enzyme (e.g., RFLP) and / or due to polymerase chain reaction techniques (e.g., STS, SSR / microsatellites, AFLP and the like). In some embodiments of the invention, all differences between the two parental genotypes are divided in the mapped population based on the cross of the given parental genotypes. You can compare the segregation of different markers, and you can calculate the frequency of recombination. Methods for mapping plant markers are described, for example, in Glick & Thompson, 1993; Zietkiewicz et al., 1994. The recombination frequencies of molecular markers on different chromosomes are usually 50%. The frequency of recombination between molecular markers located on the same chromosome generally depends on the distance between the markers. A low recombination frequency usually corresponds to a small genetic distance between markers on the chromosome. Comparison of all recombination frequencies allows one to determine the most logical order of molecular markers on chromosomes. This most logical order can be depicted on the clutch map (Paterson, 1996). A group of adjacent or sequential markers on the clutch map that is associated with improved water consumption optimization may indicate the position of the MTL associated with improved water consumption optimization. Genetic loci that correlate with certain phenotypes, such as drought tolerance, can be mapped to the body’s genome. By identifying a marker or cluster of markers that segregate together with the trait of interest, the breeder can quickly select the desired phenotype by selecting the correct marker (this process is called selection using a marker or MAS). Such markers can also be used by breeders to develop in silico genotypes and for practical selection of the whole genome.

The object of the invention disclosed herein relates in some embodiments to markers associated with increased drought tolerance / optimization of water consumption. Detection of these markers and / or other linked markers can be used to identify, select and / or produce drought tolerant plants and / or remove plants that are not drought tolerant from breeding or planting programs.

An object of the invention disclosed herein relates to markers associated with improved features for optimizing water consumption. The marker of an object of the invention disclosed herein may contain one allele or combination of alleles at one or more genetic loci. In some embodiments of the invention, one or more alleles is characterized by one or more loci selected from, but not limited to, loci represented by sequences of SEQ ID NOS: 1-117, 400, and 401, which are located in the Zea mays genome as follows:

(I) SEQ ID NO: 1 originates from the Zea mays Zmlga4 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 1 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 118; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 119; and moreover, this locus contains alleles of the trait associated with optimization of water consumption, moreover, these alleles are characterized by single nucleotide polymorphism at nucleotide positions 115, 270, 301 and 483, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6 , 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 1 on chromosome 8 Zea mays, which gives an improved trait associated with optimization of water consumption;

(II) SEQ ID NO: 2 originates from the locus of optimization of water consumption and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 2 obtained by amplification of the Zea mays nucleic acid with the first oligonucleotide, containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 120, and a second oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ I D NO: 121; and moreover, this locus contains alleles of the trait associated with optimization of water consumption, moreover, these alleles are characterized by single nucleotide polymorphism at nucleotide positions 100 and 264-271, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7 , 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 2 on chromosome 8 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(III) SEQ ID NO: 3 originates from the Zea mays ZmDr1 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 2 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 122; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 123; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by single nucleotide polymorphism at nucleotide position 216 of SEQ ID NO: 3, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 3 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(IV) SEQ ID NO: 4 originates from the Zea mays ZmDrA locus and is determined by a first oligonucleotide and a second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 4 obtained by amplification of a Zea mays nucleic acid with a first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 124; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 125; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by single nucleotide polymorphism at nucleotide position 503 of the sequence SEQ ID NO: 4, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6 , 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 4 on chromosome 7 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(V) SEQ ID NO: 5 originates from the Zea mays ZmDr2 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 4 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 126; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 127; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 818-821 of the sequence SEQ ID NO: 5, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 5 on the Zea mays chromosome 2, which gives an improved trait associated with optimizing water consumption;

(VI) SEQ ID NO: 6 originates from the Zea mays ZmDr3 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 6 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 128; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 129; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 254 of the sequence SEQ ID NO: 6, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 6 on the Zea mays chromosome 2, which gives an improved trait associated with optimizing water consumption;

(VII) SEQ ID NO: 7 originates from the Zea mays ZmDr4 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 7 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 130; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 131; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 4497-4498, 4505, 4609, 4641, 4792, 4836, 4844, 4969 and 4979-4981 of the sequence SEQ ID NO: 7, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 7 on chromosome 8 Zea mays, which gives an improved trait associated with optimizing water consumption;

(VIII) SEQ ID NO: 8 originates from the Zea mays ZmMa3 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 8 obtained by amplification of the Zea mays nucleic acid with the first oligon containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 132, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 133; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by polymorphisms at nucleotide positions 217, 390 and 477 of the sequence SEQ ID NO: 8, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 8 on the Zea mays chromosome 2, which gives an improved trait associated with optimizing water consumption;

(IX) SEQ ID NO: 9 originates from the Zea mays genome and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 9 obtained by amplification of the Zea mays nucleic acid with the first oligonucleotide, containing a nucleotide sequence as indicated by SEQ ID NO: 134; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 135; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 292 of the sequence SEQ ID NO: 9, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 9 on chromosome 4 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(X) SEQ ID NO: 10 originates from the Zea mays ZmBglcn locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 10 obtained by amplification of the Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 136, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 137; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 166 of the sequence SEQ ID NO: 10, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 10 on the Zea mays chromosome 3, which gives an improved trait associated with optimizing water consumption;

(XI) SEQ ID NO: 11 originates from the Zea mays ZmLOC locus 100276591 and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 11 obtained by amplification of the Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 138 and a second oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 139; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 148 of the sequence SEQ ID NO: 11, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 11 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(XII) SEQ ID NO: 12 originates from the Zea mays ZmDr7 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 12 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 140, and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 141; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 94 of the sequence SEQ ID NO: 12, and contains any part of the DNA sequence within 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM of SEQ ID NO: 12 on the Zea mays chromosome 1, which gives an improved trait associated with optimizing water consumption;

(XIII) SEQ ID NO: 13 originates from the Zea mays ZmDr7 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 13 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 140, and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 141; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 35, 86 and / or 89 of the sequence SEQ ID NO: 13, and contains any part of the DNA sequence within 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 13 on chromosome 1 Zea mays, which gives an improved trait associated with optimization of water consumption;

(XIV) SEQ ID NO: 14 originates from the Zea mays ZmDr8 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 14 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 142; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 143; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 432 of the sequence SEQ ID NO: 14, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM of SEQ ID NO: 14 in the Zea mays genome, which provides an improved trait associated with optimizing water consumption;

(XV) SEQ ID NO: 15 originates from the Zea mays ZmHsp70 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 15 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 144; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 145; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 753 of the sequence SEQ ID NO: 15, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 15 on the Zea mays chromosome 1, which gives an improved trait associated with optimizing water consumption;

(XVI) SEQ ID NO: 16 originates from the Zea mays ZmDr9 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 16 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 146, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 147; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 755 of the sequence SEQ ID NO: 16, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 16 on chromosome 4 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XVII) SEQ ID NO: 17 originates from the Zea mays ZmDrB locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 17 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 148, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 149; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 431 of the sequence SEQ ID NO: 17, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 17 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(XVIII) SEQ ID NO: 18 originates from the Zea mays ZmAdh1-1 locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 18 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 150, and the second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 151; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 518 of the sequence SEQ ID NO: 18, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM of SEQ ID NO: 18 on the Zea mays chromosome 1, which gives an improved trait associated with the optimization of water consumption;

(XIX) SEQ ID NO: 19 originates from the Zea mays ZmDr10 locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 19 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 152, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 153; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 182, 309, 330 and 463 of the sequence SEQ ID NO: 19, and contains any part of the DNA sequence within 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 19, which gives an improved trait associated with optimizing water consumption;

(XX) SEQ ID NO: 20 originates from the Zea mays ZmDrC locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 20 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 154, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 155; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 773-776 of the sequence SEQ ID NO: 20, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 20 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(XXI) SEQ ID NO: 21 originates from the Zea mays ZmDr5 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 21 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 156, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 157; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 61, 200 and 316-324 of the sequence SEQ ID NO: 21, and contains any part of the DNA sequence within 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 21 on chromosome 5 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXII) SEQ ID NO: 22 originates from the Zea mays ZmDrD locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 22 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 158; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID N0: 159; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 211 of the sequence SEQ ID NO: 22, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 22 on chromosome 5 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXIII) SEQ ID NO: 23, originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 23 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 160, and the second oligonucleotide containing the nucleotide sequence, as indicated by the sequence spine of SEQ ID NO: 161; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 116 and 217 of the sequence SEQ ID NO: 21, and contains any part of the DNA sequence within 1, 2, 3, 4 , 5, 6, 7, 8, 9, 10, 15, 20, or 25 cm sequence SEQ ID NO: 23 on chromosome 8 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(XXIV) SEQ ID NO: 24, originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 24 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 162, and the second oligonucleotide containing the nucleotide sequence, as indicated by the sequence awn SEQ ID NO: 163; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 746 of the sequence SEQ ID NO: 24, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 24 on chromosome 8 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXV) SEQ ID NO: 25 originates from the Zea mays ZmDr12 locus and is determined by a first oligonucleotide and a second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 25 obtained by amplification of a Zea mays nucleic acid with a first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 164, and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 165; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 562 of the sequence SEQ ID NO: 25, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 25 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XXVI) SEQ ID NO: 26, originates from the Zea mays under-consumption optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 26 obtained by amplification of Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 166, and the second oligonucleotide containing the nucleotide sequence, as indicated by the sequence awn SEQ ID NO: 167; and moreover, this locus contains alleles of a trait associated with optimizing water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 1271 of SEQ ID NO: 26, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 26 on chromosome 8 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXVII) SEQ ID NO: 27 originates from the Zea mays ZmDrE locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 27 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 168; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 169; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 64 and / or 254 of the sequence SEQ ID NO: 27, and contains any part of the DNA sequence within 1, 2, 3 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cm sequence SEQ ID NO: 27 on chromosome 8 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(XXVIII) SEQ ID NO: 28 originates from the Zea mays ZmDrF locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 28 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 170; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 171; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide positions 98, 147, 224 and / or 496 of the sequence SEQ ID NO: 28, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 28 on chromosome 9 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXIX) SEQ ID NO: 29, originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 29 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 172, and the second oligonucleotide containing the nucleotide sequence as indicated by the sequence awn SEQ ID NO: 173; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 258 of the sequence SEQ ID NO: 29, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 29 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XXX) SEQ ID NO: 30 originates from the Zea mays ZmDhn2 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 30 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 174; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 175; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 259, 296, 398 and / or 1057 of the sequence SEQ ID NO: 30, and contains any part of the DNA sequence within 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 30 on chromosome 4 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXXI) SEQ ID NO: 31 originates from the Zea mays ZmDr16 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 31 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 176, and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 177; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 239 of the sequence SEQ ID NO: 31, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 31 on chromosome 8 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(XXXII) SEQ ID NO: 32 originates from the Zea mays ZmDr17 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 32 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 178; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 179; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide position 208 of the sequence SEQ ID NO: 32, and contains any part of the DNA sequence within 1, 2, 3, 4, 5 , 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 32 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(XXXIII) SEQ ID NO: 33 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 33 obtained by amplification of Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 180; and a second oligonucleotide containing a nucleotide sequence as indicated by a sequence awns SEQ ID NO: 181; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 391 of the sequence SEQ ID NO: 33, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 33 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XXXIV) SEQ ID NO: 34 originates from the Zea mays ZmZCN6 locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 34 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 182, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 183; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 144-145, 169 and / or 537 of the sequence SEQ ID NO: 34, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 34 on chromosome 4 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXXV) SEQ ID NO: 35 originates from the Zea mays ZmDrG locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 35 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 184; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 185; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 76 of the sequence SEQ ID NO: 35, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 35 on the Zea mays chromosome 5, which gives an improved trait associated with optimizing water consumption;

(XXXVI) SEQ ID NO: 36 originates from the Zea mays ZmDhn1 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 36 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 186; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 187; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 500, 568 and / or 698 of the sequence SEQ ID NO: 36, and contains any part of the DNA sequence within 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 36 on chromosome 6 Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXXVII) SEQ ID NO: 37 originates from the Zea mays ZmDrH locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 37 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 188, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 189; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 375 and / or 386 of the sequence SEQ ID NO: 37, and contains any part of the DNA sequence within 1, 2, 3 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 37 on chromosome 5 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXXVIII) SEQ ID NO: 38 originates from the Zea mays ZmDrI locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 38 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 190; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 191; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 309 and / or 342 of the sequence SEQ ID NO: 38, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 38 on chromosome 3 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XXXIX) SEQ ID NO: 39 originates from the Zea mays ZmDrJ locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 39 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 192, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 193; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 445 of the sequence SEQ ID NO: 39, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 39 on the Zea mays chromosome 5, which gives an improved trait associated with optimizing water consumption;

(XL) SEQ ID NO: 40 originates from the Zea mays ZmH2B1 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 40 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 194, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 195; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 602 of the sequence SEQ ID NO: 40, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 40 on chromosome 4 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XLI) SEQ ID NO: 41 originates from the Zea mays ZmDr3 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 41 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 196, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 198; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 190 and / or 580 of the sequence SEQ ID NO: 41, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 41 on the Zea mays chromosome 2, which gives an improved trait associated with optimizing water consumption;

(XLII) SEQ ID NO: 42 is derived from the Zea mays ZmDrK locus. and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 42 obtained by amplification of a Zea mays nucleic acid with a first oligonucleotide containing the nucleotide sequence as indicated by SEQ ID NO: 198, and a second oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 199; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide positions 238, 266-267 and 808 of the sequence SEQ ID NO: 42, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 42 in the Zea mays genome, which gives an improved trait associated with optimizing water consumption;

(XLIII) SEQ ID NO: 43 originates from the Zea mays ZmCat1 locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 43 obtained by amplification of the Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 200; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 201; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 708 of the sequence SEQ ID NO: 43, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 43 on the Zea mays chromosome 5, which gives an improved trait associated with optimizing water consumption;

(XLIV) SEQ ID NO: 44 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, said oligonucleotides being used to amplify a subsequence of SEQ ID NO: 44 obtained by amplifying a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 202; and a second oligonucleotide containing a nucleotide sequence as indicated by STI SEQ ID NO: 203; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 266 of the sequence SEQ ID NO: 44, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM of SEQ ID NO: 44 on the Zea mays chromosome 8, which gives an improved trait associated with optimizing water consumption;

(XLV) SEQ ID NO: 45 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 45 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 202; and a second oligonucleotide containing a nucleotide sequence as indicated sequentially SEQ ID NO: 203; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 475 of the sequence SEQ ID NO: 45, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 45 on the Zea mays chromosome 8, which gives an improved trait associated with optimizing water consumption;

(XLVI) SEQ ID NO: 46 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 46 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 204, and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 205, and moreover, this locus contains alleles of the trait associated with optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 386 of the sequence SEQ ID NO: 46, and contains any part of the DNA sequence within 1, 2, 3 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 46 on chromosome 8 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(XLVII) SEQ ID NO: 47 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 47 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 206, and a second oligonucleotide containing the nucleotide sequence, as indicated by the sequence awn SEQ ID NO: 207; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 87 of the sequence SEQ ID NO: 47, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 47 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XLVIII) SEQ ID NO: 48 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 48 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence, as indicated by the sequence of SEQ ID NO: 208, and a second oligonucleotide containing a nucleotide sequence, as indicated by the sequence awns SEQ ID NO: 209; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 472 of the sequence SEQ ID NO: 48, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 48 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(XLIX) SEQ ID NO: 49 originates from the Zea mays ZmRIC1 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 49 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 210; and a second oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 211; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 166, 224, 650 and / or 892 of the sequence SEQ ID NO: 49, and contains any part of the DNA sequence within 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 49 on chromosome 8 Zea mays, which gives an improved trait associated with the optimization of water consumption;

(L) SEQ ID NO: 50 originates from the Zea mays ZmPK4 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 50 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 212; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 213; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 541 of the sequence SEQ ID NO: 50, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 50 on chromosome 8 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(LI) SEQ ID NO: 51 originates from the Zea mays ZmPK4 locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 51 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 212; and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 213; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 111 of the sequence SEQ ID NO: 51, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 51 on chromosome 8 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(LII) SEQ ID NO: 52 originates from the Zea mays Zpu1 locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 52 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 214, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 215; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 442 of the sequence SEQ ID NO: 52, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 52 on the Zea mays chromosome 2, which gives an improved trait associated with optimizing water consumption;

(LIII) SEQ ID NO: 53 originates from the Zea mays ZmDrL locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 53 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 216, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 217; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 83, 428, 491 and / or 548 of the sequence SEQ ID NO: 53, and contains any part of the DNA sequence within 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 53 on chromosome 9 of Zea mays, which gives an improved trait associated with optimization of water consumption;

(LIV) SEQ ID NO: 54 originates from the Zea mays ZmDrM locus and is determined by the first oligonucleotide and the second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of the sequence SEQ ID NO: 54 obtained by amplification of a Zea mays nucleic acid with the first oligonucleotide containing a nucleotide sequence as indicated by the sequence of SEQ ID NO: 218, and a second oligonucleotide containing the nucleotide sequence as indicated by the sequence of SEQ ID NO: 219; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 126 of the sequence SEQ ID NO: 54, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 54 on the 7 Zea mays chromosome 7, which gives an improved trait associated with optimizing water consumption;

(LV) SEQ ID NO: 55 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 55 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 220; and a second oligonucleotide containing a nucleotide sequence as indicated sequentially ti SEQ ID NO: 221; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 193 of the sequence SEQ ID NO: 55, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 55 on chromosome 8 of Zea mays, which gives an improved trait associated with optimizing water consumption;

(LVI) SEQ ID NO: 56 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 56 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 222; and a second oligonucleotide containing a nucleotide sequence as indicated sequentially SEQ ID NO: 223; and moreover, this locus contains alleles of a trait associated with optimization of water consumption, moreover, these alleles are characterized by one or more polymorphisms at nucleotide positions 237 and / or 516 of the sequence SEQ ID NO: 56, and contains any part of the DNA sequence within 1, 2, 3 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of the sequence SEQ ID NO: 56 on chromosome 8 of Zea mays, which gives an improved trait associated with the optimization of water consumption;

(LVII) SEQ ID NO: 57 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 57 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 224, and a second oligonucleotide containing a nucleotide sequence as indicated by STI SEQ ID NO: 225; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 173 of the sequence SEQ ID NO: 57, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 57 on the Zea mays chromosome 8, which gives an improved trait associated with optimizing water consumption;

(LVIII) SEQ ID NO: 58 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 58 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing the nucleotide sequence, as indicated by the sequence of SEQ ID NO: 226, and a second oligonucleotide containing the nucleotide sequence, as indicated by the sequence awn SEQ ID NO: 227; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, moreover, these alleles are characterized by polymorphism at nucleotide position 486 of the sequence SEQ ID NO: 58, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cM of SEQ ID NO: 58 on the Zea mays chromosome 8, which gives an improved trait associated with optimizing water consumption;

(LIX) SEQ ID NO: 59 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, said oligonucleotides being used to amplify a subsequence of SEQ ID NO: 59 obtained by amplifying a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence, as indicated by the sequence of SEQ ID NO: 228, and a second oligonucleotide containing a nucleotide sequence, as indicated sequentially SEQ ID NO: 229; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 729 of the sequence SEQ ID NO: 59, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 59 on chromosome 8 of Zea mays, which gives improved optimization of water consumption of associated traits; and

(LX) SEQ ID NO: 60 originates from the Zea mays water optimization locus and is determined by the first oligonucleotide and second oligonucleotide, wherein said oligonucleotides can be used to amplify a subsequence of SEQ ID NO: 60 obtained by amplification of a Zea mays nucleic acid with the first an oligonucleotide containing a nucleotide sequence as indicated by SEQ ID NO: 230; and a second oligonucleotide containing a nucleotide sequence as indicated sequentially ti SEQ ID NO: 231; and moreover, this locus contains alleles of the trait associated with the optimization of water consumption, and these alleles are characterized by polymorphism at nucleotide position 267 of the sequence SEQ ID NO: 60, and contains any part of the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 cM sequences of SEQ ID NO: 60 on chromosome 8 of Zea mays, which gives improved optimization of water consumption of associated traits; and

in some embodiments, the DNA sequence within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 cm of the marker sequence of the subject disclosed herein displays a genetic recombination rate of less than than about 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1%, with a marker of the subject disclosed herein. In some embodiments, the germplasm is a Zea mays line or variety.

DNA fragments associated with the presence of the trait, alleles and / or haplotypes associated with optimizing water consumption, including, but not limited to, the sequences of SEQ ID NOs: 1-117, 400 and 401, also relate to the present invention. In some embodiments, DNA fragments associated with the presence of a trait associated with optimizing water consumption have a predicted length and / or nucleic acid sequence, and a DNA fragment with a predicted length and / or predicted nucleic acid sequence is detected such that the amplified DNA fragment has a length that matches (plus or minus several bases, for example, a length of more or less one, two or three os IAOD), the predicted length. In some embodiments, the DNA fragment is an amplified fragment, and the amplified fragment has the same predicted length and / or nucleic acid sequence as the amplified fragment obtained by similar reaction with the same DNA primers from the plant in which the marker was first detected or a nucleic acid sequence that matches (i.e., as a nucleotide sequence identity of more than 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%) of the expected sequence based on the marker sequence associated with that attribute associated with the optimization of water consumption in the plant in which the marker was first detected. When considering the present disclosure, one skilled in the art will understand that markers that are absent in plants while they were present in at least one parent plant (so-called transmarkers) may also be applicable in assays for detecting a desired trait in a descendant plant, although testing for the absence of a marker to detect the presence of a specific trait is not optimal. Detection of an amplified DNA fragment with a predicted length or a predicted nucleic acid sequence can be performed by any of a variety of methods, including, but not limited to, standard gel electrophoresis methods and / or using automated DNA sequencers. These methods are not described in detail here, as they are well known in the art.

A primer (in some embodiments, an extension primer, and in some embodiments, an amplification primer) is, in some embodiments, single-stranded to maximize efficiency in extension and / or amplification. In some embodiments, the primer is an oligodeoxyribonucleotide. The primer is usually long enough to begin the synthesis of elongation and / or amplification products in the presence of a polymerization agent. Minimum primer lengths may depend on many factors, including, but not limited to, temperature and composition (A / T content compared to G / C) of the primer.

In connection with the amplification primer, these primers are usually provided in the form of one or more sets of bidirectional primers, which include one or more direct and one or more reverse primers widely used in the field of DNA amplification techniques, such as PCR amplification. Thus, it should be understood that the term “primer” as used herein may refer to more than one primer, especially when there is some uncertainty in the information regarding the terminal sequence (s) of the target region to be amplified. Thus, a “primer” may include a collection of primer oligonucleotides containing sequences representing possible changes in the sequence, or includes nucleotides that allow typical base pairing. Primers may be prepared by any suitable method. Methods for producing specific sequence oligonucleotides are known in the art and include, for example, cloning and restriction of the corresponding sequences and direct chemical synthesis. Chemical synthesis methods may include, for example, a phosphodiester or tri-ether method, a diethylphosphoamidate method, and a solid support method disclosed in US Pat. No. 4,545,868.

Primers can be labeled, if desired, with the inclusion of detectable fragments, for example, spectroscopic, fluorescent, photochemical, biochemical, immunochemical or chemical residues.

The matrix-dependent extension of the oligonucleotide primer is catalyzed by a polymerizing agent in the presence of sufficient amounts of four deoxyribonucleotide triphosphates (dATP, dGTP, dTTP and dTTP, i.e. dNTP) or their analogs in a reaction medium that contains the corresponding salts, metal cations and pH buffer system. Suitable polymerizing agents are enzymes that are known to catalyze primer and matrix independent DNA synthesis. Known DNA polymerases include, for example, E. coli DNA polymerase or its Klenov fragment, T4 DNA polymerase and Taq DNA polymerase, as well as various modifications thereof. The reaction conditions for catalyzing DNA synthesis with such DNA polymerases are known in the art. The synthesis products are duplex molecules consisting of matrix strands and primer extension strands, which include the desired sequence. These products, in turn, can serve as a matrix for the next replication cycle. In the second replication cycle, the primer extension strand of the first cycle is annealed with a complementary primer; the synthesis gives a “short” product that is bound at both the 5'- and 3'-ends by primer sequences or complementary sequences to them. Repeated denaturation cycles, primer annealing, and elongation can lead to exponential accumulation of the target region determined by the primers. A sufficient number of cycles are performed to achieve the desired amount of polynucleotide containing the target nucleic acid region. The desired amount can vary and is determined by the function that the produced polynucleotide serves.

The PCR method is well described in reference books and is known to those skilled in the art. After amplification by PCR, target polynucleotides can be detected by hybridization with a polynucleotide probe that forms a stable hybrid with such a target sequence under conditions of stringent and moderately stringent hybridization and washing. If the probes are expected to be almost completely complementary (i.e., about 99% or more) of the target sequence, stringent conditions can be applied. If some mismatches are expected, for example, if variant strains are expected, as a result of which the probe will not be completely complementary, then the stringency of hybridization can be reduced. In some embodiments, conditions are selected to exclude non-specific / random binding. Conditions that affect hybridization and which prevent nonspecific binding are known in the art and are described, for example, in Sambrook & Russell, 2001. Typically, lower salt concentration and high temperature increase the stringency of hybridization conditions.

In order to determine the presence of two alleles associated with the optimization of water consumption on one chromosome in a plant, methods of “painting” chromosomes can also be applied. Using such methods, at least the first allele associated with the optimization of water consumption and at least the second allele associated with the optimization of water consumption can be detected on the same chromosome by in situ hybridization or in situ PCR methods. It is more convenient that the presence of two alleles associated with the optimization of water consumption on one chromosome is confirmed by determining the degree of their linkage: that is, these signs show reduced segregation when compared with genes located on separate chromosomes.

The alleles identified in this document associated with optimizing water consumption are located on many different chromosomes or in linkage groups, and their locations can be characterized by a number of other independent markers in other respects. In these studies, single nucleotide polymorphisms (SNPs) were used, although markers based on restriction fragment length polymorphisms (RFLP), markers based on amplified fragment length polymorphism (AFLP), microsatellite markers (e.g. SSR) could also be applied and can be applied. , mutation insertion markers, known sequence amplified region (SCAR) markers, split amplified polymorphic sequence (CAPS) markers, isoenzyme markers Based on microarray technology, assays TaqMan®, analysis Illumina® GoldenGate® Assay, nucleic acid sequencing techniques or combinations of these markers.

In general, providing information on the complete sequence of alleles and / or haplotypes associated with optimizing water consumption is not necessary, since the path used for the first detection of alleles and / or haplotypes associated with optimizing water consumption allows you to track those plants among the descendant plant population which have the genetic potential to demonstrate a specific phenotypic trait. Offering a non-limiting list of markers, an object of the invention disclosed herein, therefore, relates to the effective use of the alleles and / or haplotypes associated with optimization of water consumption disclosed herein in breeding programs. In some embodiments, the marker is specific for a particular line of offspring. Thus, a particular trait can be associated with a specific marker.

Markers, as disclosed here, not only indicate the location of alleles associated with optimizing water consumption, they also correlate with the presence of a particular phenotypic trait in the plant. It should be noted that single nucleotide polymorphisms that indicate where an allele associated with optimizing water consumption is present in the genome is not a limitation. In general, the location of the allele associated with the optimization of water consumption is indicated by a set of single nucleotide polymorphisms that demonstrate a statistical correlation with a phenotypic trait. After a marker is found outside the single nucleotide polymorphism (i.e., a marker that has an LOD score below a certain threshold, indicating that this marker is so far that recombination in the region between such a marker and the allele associated with water consumption optimization is so often that the presence of the marker does not correlate statistically significantly with the presence of the phenotype), the boundaries of the allele associated with the optimization of water consumption can be considered established. Thus, it is also possible to indicate the location of the allele associated with the optimization of water consumption using other markers that are located within such a specified area. Additionally, it should be noted that single nucleotide polymorphism can also be used to indicate the presence of an allele (and therefore phenotype) associated with optimization of water consumption in a single plant, which in some embodiments of the invention means that it can be used in selection procedures using a marker ( MAS).

In principle, the number of potentially applicable markers can be very large. Any marker linked to an allele associated with optimization of water consumption (for example, falling within the physical boundaries of the genomic region between markers with established LOD scores above a certain threshold, thereby indicating that no recombination between the marker and the associated with optimization of water consumption allele appears or very little appears in crosses, as well as any marker that is disequilibrium linked to the allele associated with the optimization of water consumption, as well as markers that represent minutes of change mutation within the allele associated with optimizing water consumption) may be used in the disclosed methods and compositions, and such markers are within the scope disclosed herein subject matter. This fact means that the markers indicated in the application as associated with the allele associated with the optimization of water consumption (for example, markers that are present in or contain any of the sequences of SEQ ID NO: 1-24) are non-limiting examples of markers suitable for use in the methods and compositions disclosed herein. Moreover, when the allele associated with the optimization of water consumption, or its specific part that carries this trait, is introgressed into a different genetic background (that is, into the genome of another corn or other plant), then it is possible that some markers will no longer be found in the descendant , despite the trait present in it, indicating that such markers are located outside the genomic region, which represents a specific part that carries this trait associated with optimization of water consumption of the allele in the initial bottom of the parent line, and that the new genetic background has a different genomic organization. Such markers, the absence of which indicates the successful introduction of a genetic element into the offspring, are called "trans markers" and may be equally suitable in relation to the disclosed subject matter of this invention.

When identifying alleles and / or haplotypes associated with water consumption optimization, the effect of alleles and / or haplotypes associated with water consumption optimization (e.g., a trait) can be confirmed, for example, by evaluating a trait in progeny segregated by alleles and / or haplotypes associated with water consumption optimization. Characterization can be performed accordingly using phenotypic assessment, as is known in the art for signs of optimizing water consumption. For example, to assess the characteristics of hybrid and / or inbred maize, field studies can be conducted under natural and / or irrigated conditions.

Markers related to the disclosed subject matter of this invention can be used to detect the presence of one or more alleles and / or haplotypes of a sign of optimized water consumption at loci related to the disclosed subject matter of a corn plant suspected of having an introgressive optimization characteristic water consumption, and, therefore, can be used in methods including marker crossing and marker selection of such corn plants that are recognized to optimize water consumption. In some embodiments of the invention, the detection of the presence of an allele and / or haplotype associated with the optimization of water consumption of an object of the invention disclosed herein is performed with at least one of the markers of an allele and / or haplotype associated with the optimization of water consumption, as defined herein. Another objective of the disclosed subject matter, therefore, relates to a method for detecting the presence of an allele and / or haplotype associated with optimizing water consumption for at least one of the signs of optimizing water consumption disclosed herein and comprising detecting the presence of a nucleic acid sequence associated with optimizing the water consumption of the allele and / or haplotype in a corn plant bearing a sign of optimization of water consumption, the presence of which can be detected ENO using the disclosed markers.

In some embodiments, the detection comprises determining the nucleotide sequence of a Zea mays nucleic acid that is associated with a trait, allele and / or haplotype associated with optimizing water consumption. The task of determining the nucleotide sequence associated with the optimization of water consumption of the allele and / or haplotype of the subject matter disclosed herein can be solved, for example, by determining the nucleotide sequence of one or. more markers associated with the allele and / or haplotype associated with the optimization of water consumption, and the construction of internal primers for marker sequences, which can then be used to further determine the sequence associated with the optimization of water consumption of the allele and / or haplotype outside the marker sequences.

For example, the nucleotide sequence of SNP markers disclosed herein can be obtained by isolating the markers from an electrophoresis gel used to determine the presence of markers in the plant genome of an object of the invention, and determining the nucleotide sequence of markers, for example, by chain termination dideoxy sequencing methods that are well known in this technical field. In some embodiments of the invention pertaining to such methods for detecting the presence of alleles and / or haplotypes associated with optimization of water consumption in a characteristic maize plant, the method may also comprise providing an oligonucleotide or polynucleotide capable of hybridization under stringent hybridization conditions with a marker nucleic acid sequence, linked to associated with optimization of water consumption allele and / or haplotype, which in some embodiments of the invention is selected from the markers disclosed herein, binding of an oligonucleotide or polynucleotide to a digested genomic nucleic acid of a corn plant bearing the trait, and determining the presence of specific hybridization of the oligonucleotide or polynucleotide with the digested genomic nucleic acid. In some embodiments of the invention, the method is carried out on a nucleic acid sample obtained from a corn plant bearing this trait, although in situ hybridization methods can also be used. Alternatively, after the nucleotide sequence of the alleles and / or haplotype associated with the optimization of water consumption has been determined, one skilled in the art can construct specific hybridization probes or oligonucleotides capable of hybridization under stringent hybridization conditions with a nucleic acid sequence associated with the optimization of water consumption of the allele and / or haplotype, and may use such hybridization probes in the methods for detecting the presence of a associated with the optimization of water consumption of the allele and / or haplotype in the corn plant bearing the trait.

In some embodiments, the markers may comprise, consist essentially of, or consist of:

1) a haplotype containing allele A at positions 4979-4981 of SEQ ID NO: 7, allele A at position 472 of SEQ ID NO: 48, allele G at position 237 of SEQ ID NO: 56, allele T at position 173 of SEQ ID N0: 57, allele A at position 391 of SEQ ID NO: 33, allele G at position 116 of SEQ ID NO: 23, allele G at position 100 of SEQ ID NO: 2 and allele G at position 267 of SEQ ID NO : 60;

2) a haplotype containing allele C at position 386 of SEQ ID NO: 46, allele A at positions 4979-4981 of SEQ ID NO: 7, allele A at position 472 of SEQ ID NO: 48, allele A at position 266 of SEQ ID NO: 44, allele T at position 309 of SEQ ID NO: 19, allele G at position 111 of SEQ ID NO: 51, allele G at position 562 of SEQ ID NO: 25 and allele C at position 1271 of SEQ ID NO : 26;

3) a haplotype containing the G allele at position 87 of SEQ ID NO: 47, the allele at position 4641 of SEQ ID NO: 7, the G allele at position 472 of SEQ ID NO: 48, allele A at position 266 of SEQ ID NO: 44, allele C at position 746 of SEQ ID NO: 24, allele C at position 258 of SEQ ID NO: 29, allele A at position 217 of SEQ ID NO: 23, allele G at position 100 of SEQ ID NO: 2, allele C at position 486 of the sequence SEQ ID NO: 58 and allele G at position 193 of the sequence SEQ ID NO: 55;

4) a haplotype containing allele A at position 4641 of SEQ ID NO: 7, allele G at position 237 of SEQ ID NO: 56, allele A at position 391 of SEQ ID NO: 33, allele T at position 309 of SEQ ID NO : 19, a deletion at positions 264-271 of the sequence SEQ ID NO: 2 and allele C at position 486 of the sequence SEQ ID NO: 58;

5) a haplotype containing allele A at positions 4979-4981 of the sequence SEQ ID NO: 7 allele C at position 516 of the sequence SEQ ID NO: 56, allele T at position 475 of the sequence SEQ ID NO: 45, allele A at position 391 of the sequence SEQ ID N0: 33, allele G at position 463 of SEQ ID NO: 19, allele G at position 254 of SEQ ID NO: 27, allele G at position 729 of SEQ ID NO: 59, allele G at position 267 of SEQ ID NO: 60 and the G allele at position 193 of the sequence SEQ ID NO: 55; or

6) a haplotype containing allele A at position 4641 of SEQ ID NO: 7, allele G at position 237 of SEQ ID NO: 56, allele C at position 258 of SEQ ID NO: 29, allele G at position 463 of SEQ ID NO : 19 and the G allele at position 193 of the sequence SEQ ID NO: 55.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) a haplotype containing allele A at positions 4979-4981 of the sequence SEQ ID NO:

7, allele A at position 472 of the sequence SEQ ID NO: 48 and allele T at position 173 of the sequence SEQ ID NO: 57;

2) a haplotype containing allele C at position 386 of SEQ ID NO: 46, allele A at positions 4979-4981 of SEQ ID NO: 7, allele A at position 472 of SEQ ID NO: 48, allele A at position 266 of SEQ ID NO: 44, T allele at position 309 of SEQ ID NO: 19 and G allele;

3) a haplotype containing the allele G at position 87 of SEQ ID NO: 47, allele A at position 4641 of SEQ ID NO: 7, allele G at position 472 of SEQ ID NO: 48, allele A at position 266 of SEQ ID NO : 44, allele C at position 258 of the sequence SEQ ID NO: 29 and allele G at position 193 of the sequence SEQ ID NO: 55;

4) a haplotype containing the allele A at position 4641 of the sequence SEQ ID NO: 7 and the allele T at position 309 of the sequence SEQ ID NO: 19;

5) a haplotype containing allele A at positions 4979-4981 of SEQ ID NO: 7, allele T at position 475 of SEQ ID NO: 45, allele G at position 463 of SEQ ID NO: 19 and allele G at position 193 of SEQ ID NO: 55; or

6) a haplotype containing allele A at position 4641 of SEQ ID NO: 7, allele C at position 258 of SEQ ID NO: 29, allele G at position 463 of SEQ ID NO: 19 and allele G at position 193 of SEQ ID NO : 55.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) allele A at positions 4979-4981 of the sequence SEQ ID NO: 7;

2) allele A at position 4641 of the sequence SEQ ID NO: 7;

3) a haplotype containing the C allele at position 386 of the sequence SEQ ID NO: 46 and the allele A at positions 4979-4981 of the sequence SEQ ID NO: 7; or

4) a haplotype containing allele A at position 4641 of the sequence SEQ ID NO: 7 and allele G at position 472 of the sequence SEQ ID NO: 48.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) a haplotype containing the sequences of SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 16, SEQ ID NO: 20 and SEQ ID NO: 25;

2) a haplotype containing the sequences of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 26 and SEQ ID NO: 27;

3) a haplotype containing the sequences of SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 28;

4) a haplotype containing the sequences of SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 18, SEQ ID NO: 19 and SEQ ID NO: 21;

5) a haplotype containing the sequences of SEQ ID NO: 3, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 13, SEQ ID NO: 17, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 28; or

6) a haplotype containing the sequences of SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 14, SEQ ID NO: 17 and SEQ ID NO: 28.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) a haplotype containing the sequences of SEQ ID NO: 3, SEQ ID NO: 5 and SEQ ID NO: 11;

2) a haplotype containing the sequences of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 9, SEQ ID NO: 18 and SEQ ID NO: 22;

3) a haplotype containing the sequences of SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 14 and SEQ ID NO: 28;

4) a haplotype containing the sequences of SEQ ID NO: 4, SEQ ID NO: 9 and SEQ ID NO: 18;

5) a haplotype containing the sequences of SEQ ID NO: 3, SEQ ID NO: 10, SEQ ID NO: 17 and SEQ ID NO: 28; or

6) a haplotype containing the sequences of SEQ ID NO: 4, SEQ ID NO: 14, SEQ ID NO: 17 and SEQ ID NO: 28.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) the sequence of SEQ ID NO: 3;

2) the sequence of SEQ ID NO: 4;

3) a haplotype containing the sequences of SEQ ID NO: 2 and SEQ ID NO: 3 or

4) a haplotype containing the sequences of SEQ ID NO: 4, SEQ ID NO: 6.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 100, SEQ ID NO: 104 and SEQ ID NO: 109;

2) a haplotype containing the sequences of SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 93, SEQ ID NO: 102, SEQ ID NO: 106, SEQ ID NO: 110 and SEQ ID NO: 111;

3) a haplotype containing the sequences of SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 93, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 104, SEQ ID NO: 105 and SEQ ID NO: 112;

4) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 97, SEQ ID NO: 102, SEQ ID NO: 103 and SEQ ID NO: 105;

5) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 97, SEQ ID NO: 101 SEQ ID NO: 107, SEQ ID NO: 108 SEQ ID NO: 109 and SEQ ID NO: 112 or

6) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 91, SEQ ID NO: 98, SEQ ID NO: 101 and SEQ ID NO: 112.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 89 and SEQ ID NO: 95;

2) a haplotype containing the sequences of SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 93, SEQ ID NO: 102 and SEQ ID NO: 106;

3) a haplotype containing the sequences of SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 93, SEQ ID NO: 98 and SEQ ID NO: 112;

4) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 93 and SEQ ID NO: 102;

5) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 94, SEQ ID NO: 101 and SEQ ID NO: 112 or

6) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 98, SEQ ID NO: 101 and SEQ ID NO: 112.

In some embodiments, a marker may comprise, consist essentially of, or consist of:

1) the sequence of SEQ ID NO: 87;

2) the sequence of SEQ ID NO: 88;

3) a haplotype containing the sequences of SEQ ID NO: 86 and SEQ ID NO: 87; or

4) a haplotype containing the sequences of SEQ ID NO: 88 and SEQ ID NO: 90.

Certain nucleotides that are present at specific places in the markers and nucleic acids disclosed herein can be determined using standard molecular biology methods, including, but not limited to, amplification of genomic DNA from plants and subsequent sequencing. In addition, oligonucleotide primers can be developed from which specific hybridization with specific sequences can be expected, which include the polymorphisms disclosed herein. For example, you can develop oligonucleotides that distinguish the allele "A" and the allele "G" at the nucleotide position that corresponds to position 270 of the sequence SEQ ID NO: 1 using oligonucleotides containing, consisting mainly or consisting of sequences SEQ ID NO: 232 and 233. The corresponding difference between the sequences of SEQ ID NO: 232 and 233 is that the first sequence has a nucleotide G at position 19 and the second sequence has a nucleotide T at position 19. Thus, hybridization conditions can be developed after sequence of SEQ ID NO: 232, which would allow SEQ ID NO: 232 to specifically hybridize to the allele, "the G", if it is present, but does not hybridize with an allele "A" if there is an allele "A". Thus, hybridization using the data of two primers that differ only in one nucleotide can be used to analyze the presence of a particular allele at the nucleotide position corresponding to position 270 of the sequence SEQ ID NO: 1.

In some embodiments, alleles containing a marker associated with increased drought tolerance are detected using a variety of probes selected from the group consisting of:

(I) SEQ ID NO: 348 and 349; SEQ ID NO: 350 and 351; SEQ ID NO: 360 and 361; SEQ ID NO: 372 and 373; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; SEQ ID NO: 382 and 383; and SEQ ID NO: 398 and 399;

(II) SEQ ID NO: 350 and 251; SEQ ID NO: 356 and 357; SEQ ID NO: 364 and 365; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(III) SEQ ID NO: 348 and 349; SEQ ID NO: 352 and 353; SEQ ID NO: 358 and 359; SEQ ID NO: 362 and 363; SEQ ID NO: 370 and 371; SEQ ID NO: 374 and 375; SEQ ID NO: 382 and 383; SEQ ID NO: 386 and 387; and SEQ ID NO: 394 and 395;

(IV) SEQ ID NO: 346 and 347; SEQ ID NO: 352 and 353; SEQ ID NO: 356 and 357; SEQ ID NO: 372 and 373; SEQ ID NO: 388 and 389; and SEQ ID NO: 394 395;

(V) SEQ ID NO: 351 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 368 and 369; SEQ ID NO: 372 and 373; SEQ ID NO: 376 and 377; SEQ ID NO: 386 and 387; SEQ ID NO: 390 and 391; SEQ ID NO: 396 and 397; and SEQ ID NO: 398 and 399;

(VI) SEQ ID NO: 352 and 353; SEQ ID NO: 354 and 355; SEQ ID NO: 370 and 371; SEQ ID NO: 386 and 387; SEQ ID NO: 388 and 389;

(VII) SEQ ID NO: 350 and 351; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; and SEQ ID NO: 392 and 393;

(VIII) SEQ ID NO: 350 and 351; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(IX) SEQ ID NO: 352 and 353; SEQ ID NO: 370 and 371; SEQ ID NO: 380 and 381; SEQ ID NO: 382 and 383; and SEQ ID NO: 386 and 387;

(X) SEQ ID NO: 352 and 353; SEQ ID NO: 356 and 357; and SEQ ID NO: 388 and 389;

(XI) SEQ ID NO: 350 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 376 and 377; and SEQ ID NO: 386 and 387;

(XII) SEQ ID NO: 350 and 351;

(XIII) SEQ ID NO: 352 and 353;

(XIV) SEQ ID NO: 350 and 351 and SEQ ID NO: 378 and 379; and

(XV) SEQ ID NO: 352 and 353; and SEQ ID NO: 382 and 383.

In some embodiments of the invention, the marker may comprise, consist essentially of, or consist of the reverse complement of any of the above markers. In some embodiments of the invention, one or more alleles that make up the marker haplotype is present as described above, while one or more other alleles that make up the marker haplotype is present as a reverse complement to the allele (s) described above. In some embodiments, each of the alleles that make up the marker haplotype is present as an inverse complement to the allele (s) described above. In some embodiments, a marker may comprise, consist essentially of, or consist of an informative fragment of any of the above markers, a back complement of any of the above markers, or an informative fragment of a reverse complement of any of the above markers. In some embodiments of the invention, one or more alleles / sequences that make up the marker haplotype is present as described above, while one or more other alleles / sequences that make up the marker haplotype is present as an inverse complement of informative fragments of alleles / sequences described above. In some embodiments, one or more alleles / sequences that make up the marker haplotype is present as described above, while one or more other alleles / sequences that make up the marker haplotype is present as an informative fragment of the alleles / sequences described above. In some embodiments, one or more alleles / sequences that make up the marker haplotype is present as described above, while one or more other alleles / sequences that make up the marker haplotype is present as an informative fragment of the reverse complement of the alleles / sequences described above. In some embodiments, each of the alleles / sequences that make up the marker haplotype is present as an informative fragment of the alleles / sequences described above, a backward complement of alleles / sequences described above, or an informative fragment of the reverse complement of alleles / sequences described above.

In some embodiments of the invention, the marker may comprise, consist essentially of, or consist of any markers linked to the aforementioned markers. That is, any allele and / or haplotype that is non-equilibrium linked to any of the aforementioned markers can be used to identify, select and / or produce a corn plant with increased drought tolerance. Concatenated tokens can be defined, for example, using resources available on the MaizeGDB website.

Isolated and purified markers associated with increased drought tolerance also relate to the present invention. Such markers may comprise, consist essentially of, or consist of the nucleotide sequence set forth in any of the sequences of SEQ ID NOS: 1-117, 400 and 401, their reverse complement, or their informative fragment. In some embodiments of the invention, the marker contains a detectable fragment. In some embodiments of the invention, the marker allows you to detect one or more alleles of the marker indicated in this document.

Compositions containing a pair of primers capable of amplifying a sample of a nucleic acid isolated from a corn plant or germplasm to generate a marker associated with increased drought tolerance also relate to the present invention. In some embodiments of the invention, the marker contains a nucleotide sequence, as set forth here, its reverse complement or an informative fragment. In some embodiments, the marker contains a nucleotide sequence that is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% 97%, 99% or 100% identical to the nucleotide sequence set forth herein, its reverse complement or informative fragment. In some embodiments, a pair of primers is one of the pairs of amplification primers shown in Table 1 above. One skilled in the art will understand how to select alternative primer pairs according to methods well known in the art.

Table 5 summarizes the favorable alleles and single-locus haplotypes that are linked to the optimization of water consumption.

Table 5 Illustrative summary of alleles and one-locus haplotypes SEQ ID NO: Position Favorable * HAPL ** HAPL CODE one 115 G A 270 A (Y) A 301 T 483 A 2 one hundred G 264-271 DEL 3 216 G (y) four 503 A (Y) 5 818-821 INS (Y) 6 254 G (Y); A (P) 7 4497-4498 GA (Y) DEL AT 4505 G 4609 T 4641 A (Y); A A 4792 C (Y); T (Y) T 4836 T (Y) T

SEQ ID NO: Position Favorable * HAPL ** HAPL CODE 4844 FROM 4969 G 4979-4981 A (Y); G (y) Tcc 8 217 A P) A 390 G FROM 477 A 9 292 C (Y); C (P) 10 166 A (Y); A (P) eleven 148 G (p) 12 94 C (Y); C 13 35 A (P) 86 C (Y); C 89 G (y) fourteen 432 G (p) fifteen 753 A (Y) 16 755 G (y) 17 431 G (y) eighteen 518 G (P); T (W) 19 182 A (P) G D 309 A (Y); A A 330 G 463 G; C (P) G twenty 773-776 C (Y); C (P) 21 61 FROM 200 FROM E 316-324 T (Y) DEL 22 211 G (p) 23 116 G 217 A

SEQ ID NO: Position Favorable * HAPL ** HAPL CODE 24 746 FROM 25 562 G (Y); G (P); G 26 1271 FROM 27 64 G F 254 C; T (Y); C (P) T 28 98 FROM G 147 T 224 from 496 T (Y) t 29th 258 FROM thirty 259 T (R) t N 296 t 398 G (y) BUT 1057 FROM 31 239 G (Y); G (p) 32 208 G (y) 33 391 A 34 144-145 C (Y); C (P) 169 T (Y) 537 A (P) 35 76 G (y) 36 500 FROM 568 G I 698 T (Y) T 37 375 A 386 A (P); G (Y); A (Y) 38 309 C (P) 342 A (P) 39 445 G (Y); C (P)

SEQ ID NO: Position Favorable * HAPL ** HAPL CODE 40 602 A (Y) 41 190 G (Y); A (P) 580 C (Y) 42 238 A 266-268 INS (Y) DEL J 808 FROM 43 708 C (P); A (Y) 44 266 A 45 475 T 46 386 FROM 47 87 G 48 472 A; G 49 166 FROM K 224 A 650 G (Y); G (p) G 892 G fifty 541 T (Y); A (Y) 51 111 G 52 442 C; G 53 83 FROM L 428 C (P); T (Y) FROM 491 C (Y); C (P) FROM 548 FROM 54 126 A (Y) 55 193 G 56 237 G 516 FROM 57 173 T 58 486 FROM 59 729 G

SEQ ID NO: Position Favorable * HAPL ** HAPL CODE 60 267 G 400 83 FROM FROM 119 BUT BUT M 601 T T * (Y): YGSMN; (P): GMSTP, (W): GWTPN
** HAPL refers to single-locus haplotypes (that is, haplotypes that contain favorable alleles present together are specifically grouped).

The expression “haplotype code” as used herein means a set of SNPs present in a plant, with each favorable allele listed in the single-focus haplotype column of Table 5 being present in the plant. For example, it is said that a plant has “haplotype A” when at least one locus corresponding to the sequence of SEQ ID NO: 1 in the plant has G at nucleotide position 115, A at position 270 of the sequence SEQ ID NO: 1, T in nucleotide positions 301 and A at position 483. Haplotype A may alternatively be called "GATA" in relation to the data for specific nucleotide positions. Similarly, a plant is said to have “haplotype C” if at least one locus corresponding to the sequence of SEQ ID NO: 8 in the plant has A at nucleotide position 217, G at nucleotide position 290, and A at nucleotide position 477 of SEQ ID NO: 8. Haplotype C, therefore, may alternatively be referred to as “AGA” in relation to these particular nucleotide positions.

Identification of plants with various alleles and / or haplotypes of interest may provide starting material for combining alleles and / or haplotypes in descendant plants using cross-breeding strategies to “summarize” alleles and / or haplotypes. As used herein, the term “summation” and its grammatical variants refers to the intentional accumulation in plants by crossing (including, but not limited to, crossing two plants, self-pollination of one plant and / or the creation of a double haploid from one plant) favorable haplotypes for optimizing water consumption, so that the genome plants has at least one additional favorable haplotype for optimizing water consumption compared to its immediate predecessor (s).

Summation includes, in some embodiments, transferring one or more traits, alleles and / or haplotypes of water consumption optimization to a descendant corn plant, so that the descendant corn plant includes more traits, alleles and / or haplotypes of water consumption optimization, than any of the parents from whom it was derived. By way of example, but not limitation, if parent 1 has haplotypes A, B, and C and parent 2 has haplotypes D, E, and F, then “summation” refers to the production of a plant that has any of A, B, and C with any combination D, E and F. In particular, in some embodiments, “summation” refers to the production of a plant that has A, B and C, as well as one or more D, E, F, or the production of a plant that has D, E , F, as well as one or more A, B, and C. In some embodiments, “summation” refers to plant production crossing two parents of which contains all associated haplotypes optimizing water consumption, which has any of the parents.

In some embodiments, the sign of optimizing water consumption is grain yield - drought, and the favorable haplotype contains a nucleotide sequence containing T at nucleotide position 301, G at nucleotide position 115, A at nucleotide position 483, and A at nucleotide position 270 of the sequence SEQ ID NO : one; TCC trinucleotide at nucleotide positions 4979-4981, G at nucleotide position 4969, A at nucleotide position 4641, T at nucleotide position 4609, deletion of nucleotide positions 4497-4498, T at nucleotide position 4792, T at nucleotide position 4836, G at nucleotide position 4505 and C at nucleotide position 4844 of the sequence SEQ ID NO: 7; And at nucleotide position 217, G at nucleotide position 390 and A at nucleotide position 477 of SEQ ID NO: 8, G at nucleotide position 463, G at nucleotide position 330, G at nucleotide position 182 and A at nucleotide position 309 ID NO: 19; G at nucleotide position 64 and A at nucleotide position 254 of the sequence SEQ ID NO: 27; C at nucleotide position 98, T at nucleotide position 147, C at nucleotide position 224 and T at nucleotide position 496 of the sequence SEQ ID NO: 28; C at nucleotide position 500, G at nucleotide position 568, and T at nucleotide position 698 of the sequence SEQ ID NO: 36; a deletion of nucleotide positions 266-267, C at nucleotide position 808 and A at nucleotide position 238 of the sequence SEQ ID NO: 42; and / or C at nucleotide position 166, A at nucleotide position 224, G at nucleotide position 650 and G at nucleotide position 892 of the sequence SEQ ID NO: 49.

In some embodiments, the sign of optimizing water consumption is “grain yield — good irrigation,” and the favorable haplotype comprises a nucleotide sequence containing A at nucleotide position 217, G at nucleotide position 390, and A at nucleotide position 477 of SEQ ID NO: 8, C at nucleotide position 500, G at nucleotide position 568, and T at nucleotide position 698 of the sequence SEQ ID NO: 36; and / or C at nucleotide position 83, C at nucleotide position 548, C at nucleotide position 491, and C at nucleotide position 428 of the sequence SEQ ID NO: 53.

In some embodiments of the invention, the sign of optimizing water consumption is “yield reduction — hybrid,” and the favorable haplotype comprises a nucleotide sequence containing C at nucleotide position 98, T at nucleotide position 147, C at nucleotide position 224, and T at nucleotide position 496 of the SEQ sequence ID NO: 28.

In some embodiments of the invention, the sign of optimizing water consumption is a decrease in yield — inbred, and the favorable haplotype contains a nucleotide sequence containing the TCC trinucleotide at nucleotide positions 4979-4981, G at nucleotide position 4969, A at nucleotide position 4669, T at nucleotide position 4609, a deletion of nucleotide positions 4497-4498, T at nucleotide position 4792, T at nucleotide position 4836, G at nucleotide position 4505 and C at nucleotide position 4844 of the sequence SEQ ID NO: 7; And at nucleotide position 217, G at nucleotide position 390 and A at nucleotide position 477 of SEQ ID NO: 8, G at nucleotide position 64 and A at nucleotide position 254 of SEQ ID NO: 27; and / or C at nucleotide position 83, C at nucleotide position 548, C at nucleotide position 491, and C at nucleotide position 428 of the sequence SEQ ID NO: 53.

In some embodiments, the sign of optimizing water consumption is an ASI, and the favorable haplotype comprises a nucleotide sequence containing the TCC trinucleotide at nucleotide positions 4979-4981, G at nucleotide position 4969, A at nucleotide position 4641, T at nucleotide position 4609, a deletion of nucleotide positions 4497-4498, T at nucleotide position 4792, T at nucleotide position 4836, G at nucleotide position 4505, and C at nucleotide position 4844 of the sequence SEQ ID NO: 7.

In some embodiments, the sign of optimizing water consumption is the percentage of infertile plants, and the favorable haplotype contains a nucleotide sequence containing the TCC trinucleotide at nucleotide positions 4979-4981, G at nucleotide position 4969, A at nucleotide position 4669, T at nucleotide position 4609, deletion nucleotide positions 4497-4498, T at nucleotide position 4792, T at nucleotide position 4836, G at nucleotide position 4505 and C at nucleotide position 4844 of the sequence SEQ ID NO: 7; G at nucleotide position 463, G at nucleotide position 330, G at nucleotide position 182, and A at nucleotide position 309 of the sequence SEQ ID NO: 19; C at nucleotide position 61, C at nucleotide position 200 and a deletion of nucleotide positions 316-324 of the sequence SEQ ID NO: 21; and / or A at nucleotide position 398, T at nucleotide position 296, T at nucleotide position 259, and C at nucleotide position 1057 of the sequence SEQ ID NO: 30.

In some embodiments of the disclosed subject matter, the genes of Zea mays inbred or hybrid plants comprise at least three, four, five, six, seven, eight, or nine haplotypes AM, the haplotypes AM being associated with water consumption optimization and determined in this document. In some embodiments, the Zea mays inbred or hybrid plant comprises a genome containing haplotypes C, D, and G; haplotypes C, D and L, haplotypes C, G, H; haplotypes C, G and I; haplotypes C, I and L; haplotypes E, G and I, haplotypes F, G and H; haplotypes A, C, F and G; haplotypes C, E, H and I; haplotypes C, G, H and I; haplotypes C, H, I and K; haplotypes C, H, I and L; haplotypes E, F, G and H; haplotypes A, C, G, H and I; haplotypes B, C, D, G and L; haplotypes C, E, G, H and I; haplotypes C, G, H, I and L; haplotypes A, C, G, H, I and K; haplotypes C, E, F, G, H, I, J, K and L, haplotypes C, D, G and M; haplotypes C, D, L and M; haplotypes C, G, H and M; haplotypes C, G, I and M; haplotypes C, I, L, M; haplotypes E, G, I and M; haplotypes F, G, H and M; haplotypes A, C, F, G and M; haplotypes C, E, H, I and M; haplotypes C, G, H, I and M; haplotypes C, H, I, K and M; haplotypes C, H, I, L and M; haplotypes E, F, G, H and M; haplotypes A, C, G, H, I and M; haplotypes B, C, D, G, L and M; haplotypes C, E, G, H, I and M; haplotypes C, G, H, I, L and M; haplotypes A, C, G, H, I, K, M; and haplotypes C, E, F, G, H, I, J, K, L, and M. In some embodiments of the invention, an inbred or hybrid Zea mays plant is a hybrid plant that is homozygous for at least one of A- haplotypes M.

In some embodiments, the Zea mays inbred or hybrid plant comprises a genome containing haplotypes A, C, E, G, H, and I, optionally further comprising haplotype M; haplotypes B, C, D, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H and L, optionally additionally containing haplotype M; haplotypes B, C, D, G, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G and H, optionally additionally containing haplotype M; haplotypes D, E, F, G and H, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, E, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, G, H, I, and K, optionally additionally containing haplotype M; haplotypes C, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H and I, optionally additionally containing haplotype M; haplotypes A, C, E, F, G, H, I and K, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; haplotypes B, C, D, E, F, G, H and L, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I, J, K and L, optionally additionally containing haplotype M; haplotypes C, D, G, H and L, optionally additionally containing haplotype M; haplotypes C, E, F, G, H, I and L, optionally additionally containing haplotype M; and / or haplotypes B, C, D, E, G, I and L, optionally additionally containing haplotype M.

As used here, a plant that contains several haplotypes can be indicated by a code indicating the haplotypes it has. So, for example, a plant that contains at least one copy of the haplotypes C, D, E, F, G, H, I, J, K and L in its genome can be designated as "CDEFGHIJKL"; a plant that contains at least one copy of haplotypes B, C, D, E, F, G, H, I, J, K and L in its genome can be designated as "BCDEFGHIJKL", etc. In some embodiments, uppercase and lowercase letters are used to further define these haplotypes by which the plant (or its cell) is either homozygous (e.g., uppercase letters) or heterozygous (e.g., lowercase letters). By way of example, and not limitation, a plant or cell called CDEFGHIJKL has at least one of the haplotypes C, D, E, F, G, H, I, J, K, and L. In some embodiments, this designation will indicate that the plant or cell is homozygous for each of these haplotypes. Similarly, the designation cdefghijkl indicates that the plant or cell is heterozygous for the haplotypes C, D, E, F, G, H, I, J, K and L. And finally, the designation CdeFGhijKL indicates that the plant or the cell is homozygous for haplotypes C, F, G, K, and L, I and is heterozygous for haplotypes D, E, H, I, and J. In some embodiments, this designation further indicates that the plant or cell lacks haplotypes A and B, although in some embodiments of the invention, this designation indicates that then the status of the plant or cell with respect to these haplotypes is unknown or not tested.

III. Methods for introgression of alleles of interest and determination of plants containing such alleles

III.A. General principles of marker selection

Markers can be used in a variety of plant crossing applications. See, for example, Staub et al., Hortscience 31: 729 (1996); Tanksley, Plant Molecular Biology Reporter 1: 3 (1983). One of the main areas of interest is to increase the efficiency of backcrossing and introgression of genes using marker selection (MAS). Typically, MAS takes advantage of genetic markers that have been identified as separating with a high degree of probability along with the desired trait. It is assumed that such markers are located in the gene (s) / near the gene (s), which lead to the desired phenotype, and their presence indicates that the plant will have the desired trait. Plants with a marker are expected to transmit the desired phenotype to their offspring.

A marker that demonstrates linkage with a locus that affects the desired phenotypic trait is a useful tool for selecting a trait in a plant population. This is especially true when the phenotype is difficult to analyze or occurs at a late stage of plant development. Since DNA marker analyzes have become less time-consuming and require less physical space than field phenotyping, much larger populations can be analyzed, increasing the chances of finding a recombinant with the target segment from the donor line moved to the recipient line. The higher the degree of linkage, the more applicable the marker is, since the recombination between the marker and the gene that causes or provides the trait is less likely. The presence of flanking markers reduces the likelihood that false positive selection will occur. Ideally, the marker is located in the gene itself, so that recombination cannot occur between the marker and the gene. Such a marker is called an "ideal marker."

When a gene is introgressed using MAS, not only the gene is introduced, but also the flanking regions. Gepts, Crop Sci 42: 1780 (2002). This phenomenon is called linkage drag. In the case where the donor plant and the recipient plant are very distantly related, these flanking regions carry additional genes that can encode agronomically undesirable traits. This "resistance due to gene linkage" can also lead to lower yields or other negative agronomic traits even after repeated cycles of backcrossing to produce an elite line of corn. This phenomenon is also sometimes referred to as “yield drag due to gene adhesion.” The size of the flanking region can be reduced by additional backcrossing, although it is not always successful, as breeders do not control the size of this region or recombination control points. Young et al., Genetics 120: 579 (1998). Recombinations that contribute to a decrease in the size of the donor segment are usually selected in classical selection only randomly. Tanksley et al., Biotechnology 7: 257 (1989). Even after 20 return crosses, it can be expected that a significant portion of the donor chromosome will still be found, still linked to the gene to be selected. However, using markers, it is possible to isolate those rare individuals in which recombination has occurred near the genes of interest. For 150 backcross plants, there is a 95% probability that a crossover will occur in at least one plant within 1 cm of the gene, based on the distance on the map after one meiosis. Markers allow unambiguous identification of such individual plants. With one additional backcross of 300 plants, there would be a crossover probability of 95% within 1 cm of the distance on the map after one meiosis on the other side of the gene, giving a segment around the target gene of less than 2 cm based on the distance on the map after one meiosis. Such a result can be achieved with markers in two generations, whereas without markers an average of 100 generations would be required. See Tanksley et al., Above. When the exact location of the genes is known, flanking markers surrounding the gene can be used to select for recombination in populations of various sizes. For example, it can be expected that in populations of smaller sizes, recombination is expected even further from the gene, so more distal flanking markers will be required to detect recombination.

The presence of integrated corn genome linkage maps containing elevated densities of commonly available corn markers facilitated genetic mapping of maize and MAS. See, for example, the IBM2 Neighbors cards that are available online at the MaizeGDB website.

Of all types of molecular markers, SNPs are the most common and have the potential to provide the highest resolution of the genetic map. Bhattramakki et al., Plant Molec. Biol. 48: 539 (2002). SNPs can be analyzed in the so-called “super-high performance” mode because they do not require a large amount of nucleic acids, and automation of the analysis is simple. SNPs also have the advantage of using relatively inexpensive systems. These three factors together make SNPs very attractive for use in MAS. There are several methods for genotyping SNPs, including, but not limited to, hybridization, primer extension, oligonucleotide donation, nuclease digestion, minisequencing, and encoded spheres. Such methods have been considered in various publications: Gut, Hum. Mutat. 17: 475 (2001); Shi, Clin. Chem. 47: 164 (2001); Kwok, Pharmacogenomics 1:95 (2000); Bhattramakki and Rafalski, Discovery and application of single nucleotide polymorphism markers in plants, in PLANT GENOTYPING: the DNA FINGERPRINTING OF PLANTS, CABI Publishing, Wallingford (2001). A wide range of commercially available technologies use data and other SNP analysis methods, including Masscode ™ (Qiagen, Germantown, MD), Invader® (Hologic, Madison, WI), Snapshot® (Applied Biosystems, Foster City, CA), Taqman® ( Applied Biosystems, Foster City, CA) and Beadarrays ™ (Illumina, San Diego, CA).

A set of SNPs within the sequence or encompassing linked sequences can be used to describe the haplotype for any particular genotype. Ching et al., BMC Genet. 3: 19 (2002); Gupta et al., (2001), Rafalski, Plant Sci. 162: 329 (2002b). Haplotypes may be more informative than single SNPs, and may better describe any particular genotype. For example, a single SNP may be the “T” allele for a particular drought tolerant line or variety, but the “T” allele can also be found in a corn population taken for breeding, being used for recurrent parents. In this case, the combination of alleles on linked SNPs may be more informative. After a unique haplotype has been assigned to the donor chromosome region, this haplotype can be used in such a population or a subset of it to determine whether an individual has a detected gene. The use of automated high-throughput marker detection platforms known to those skilled in the art makes this process very efficient and effective.

Markers of the subject matter disclosed herein can be used in marker selection protocols to identify and / or select offspring with increased drought tolerance. Such methods may comprise, consist essentially of or consist of crossing a first corn plant or germplasm with a second corn plant or germplasm, wherein the first corn plant or germplasm contains a marker associated with increased drought tolerance and breeding offspring plants possessing this marker. Any of the first and second corn plants or both plants may be a non-naturally occurring variety of corn. In some embodiments, the first corn plant or germplasm is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, the genome of the first corn plant or germplasm is at least about 50% , 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments, the second corn plant or germplasm is an elite variety of corn. In some embodiments, the genome of the second corn plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97% , 99% or 100% identical to that of the elite variety of corn. In some embodiments, the second corn plant is a variety of NP2391. In some embodiments, the genome of the second corn plant is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of NP2391.

III.B. Methods of introgression of alleles and / or haplotypes of interest

Thus, in some embodiments, an object of the invention disclosed herein relates to methods of introgression of an allele associated with increased drought tolerance into a genetic background in which the said allele is absent. In some embodiments of the invention, the methods comprise crossing a donor containing said allele with a recurrent parent who lacks said allele, and re-crossing the offspring containing said allele with a recursive parent, said descendants being identified by the presence of a haplotype associated with them in their genomes with increased drought tolerance, wherein said haplotype is selected from the group consisting of:

nucleotide G at a position that corresponds to position 100 of the sequence SEQ ID NO: 2, trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, nucleotide A at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide T in position cat paradise corresponds to position 173 sequence SEQ ID NO: 57 and the nucleotide G at a position which corresponds to position 267 sequence SEQ ID NO: 60;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 562 of the sequence SEQ ID NO: 25, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at the position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A in position to which corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position which corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide G at a position that corresponds to position 100, nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 217 of SEQ ID NO: 23, nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide G at the position that corresponds to position 472 of the last successive SEQ ID NO: 48, a nucleotide G at a position which corresponds to position 193 sequence SEQ ID NO: 55 and the nucleotide C at a position which corresponds to position 486 sequence SEQ ID NO: 58; a nucleotide deletion at a position that corresponds to positions 264-271 of SEQ ID NO: 2, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, and nucleotide C at the position that corresponds to position 486 of the sequence SEQ ID NO: 58;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 254 of the sequence SEQ ID NO: 27, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, nucleotide G at the position that corresponds to position 193 of the sequence SEQ ID NO: 55, nucleotide C in position cat the original corresponds to position 516 of the sequence SEQ ID NO: 56, nucleotide G at the position that corresponds to position 729 of the sequence SEQ ID NO: 59, and nucleotide G at the position that corresponds to position 267 of the sequence SEQ ID NO: 60; nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55, and a nucleotide G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 472 of SEQ ID NO: 48, nucleotide A at a position that corresponds to position 237 of SEQ ID NO: 56, and nucleotide T at a position which corresponds to position 173 of the sequence SEQ ID NO: 57;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position that corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at the position that corresponds to position 87 of the sequence SEQ ID NO: 47, nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48, and a nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide A at a position that corresponds to position 309 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, and nucleotide G at a position which corresponds to position 193 of the sequence SEQ ID NO: 55;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7;

nucleotide A at a position that corresponds to position 4641 of the sequence of SEQ ID NO: 7;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, and nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, and nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48,

and their combinations,

thereby producing a drought tolerant corn plant or germplasm containing said allele associated with increased drought tolerance in the genetic background of recurrent parents, thereby introgressing an allele associated with increased drought tolerance into a genetic background in which the said allele is absent. In some embodiments, the genome of said drought tolerant corn plant or germplasm containing said allele associated with increased drought tolerance is at least about 95% identical to that of recurrent parents. In some embodiments, either the donor or the recurrent parent, or both, is an unnatural corn variety.

In some embodiments of the invention related to the methods disclosed herein, the genome of said donor is at least 95% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments, the donor is selected from a group consisting of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 and Tuxpeno VEN 692. In some embodiments, the genome of said recurrent parent plant or germplasm is at least 95% identical to that of the elite variety of maize. In some embodiments, said recurrent parent is an elite variety of corn. In some embodiments of the invention 23. the method according to item 21 or item 22, wherein said elite variety of corn is NP2391.

III.D. Methods for stacking alleles and / or haplotypes of interest

The object of the invention disclosed herein relates, in some embodiments, to "stacking" haplotypes associated with optimizing water consumption to produce plants (and parts thereof) that have numerous favorable haplotypes for optimizing water consumption. By way of example, but not limitation, an object of the invention disclosed herein relates, in some embodiments, to the identification and characterization of Zea mays loci, each of which is associated with one or more signs of optimizing water consumption. Such loci correspond to the sequences of SEQ ID NO: 1-413.

Favorable haplotypes were identified for each of these loci, which are associated with signs of optimization of water consumption. These favorable haplotypes are provided herein. An object of the invention disclosed herein relates to illustrative haplotypes that are associated with an increase and decrease in various signs of optimizing water consumption, as defined herein. The expression “favorable haplotype” means a haplotype, which leads to a quantitatively increased optimization of water consumption, compared with the case when there is an “unfavorable haplotype”. It should be noted, however, that in the case where lower optimization of water consumption is desired, the haplotypes disclosed herein as “favorable” may be unfavorable haplotypes. Thus, as used here, “favorable” is used in the context of increased optimization of water consumption and will be reviewed in the context of reduced optimization of water consumption.

III.E. Methods for identifying plants containing alleles and / or haplotypes of interest

Methods for identifying a drought tolerant corn plant or germplasm may include detecting the presence of a marker associated with increased drought tolerance. The marker can be found in any sample taken from a plant or germplasm, including, but not limited to, a whole plant or germplasm, a portion of said plant or germplasm (e.g., a cell from said plant or germplasm) or a nucleotide sequence from said plants or germplasm. The corn plant may be a non-naturally occurring corn variety. In some embodiments, the corn plant genome or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of the elite variety of corn. In some embodiments, the corn plant genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% 97%, 99%, or 100 % identical to that of NP2391.

In some embodiments of the invention, an object of the invention disclosed herein relates to methods of introgression of the locus of interest alleles associated with a sign of optimizing water consumption into a Zea mays germplasm. In some embodiments of the invention, the methods comprise:

(a) breeding a Zea mays plant that contains an allele of interest of a locus associated with a sign of water consumption optimization, the allele being determined by at least one marker allele containing a polymorphic site identified by PCR amplification of a Zea mays nucleic acid with a pair of oligonucleotide primers selected from a pair of primers 1 represented by a primer containing the sequence of SEQ ID NO: 118 and a primer containing the sequence of SEQ ID NO: 119; a pair of primers 2 represented by a primer containing the sequence of SEQ ID NO: 120 and a primer containing the sequence of SEQ ID NO: 121; a pair of primers 3 represented by a primer containing the sequence of SEQ ID NO: 122 and a primer containing the sequence of SEQ ID NO: 123; a pair of primers 4 represented by a primer containing the sequence of SEQ ID NO: 124 and a primer containing the sequence of SEQ ID NO: 125; a pair of primers 5 represented by a primer containing the sequence of SEQ ID NO: 126 and a primer containing the sequence of SEQ ID NO: 127; a pair of primers 6 represented by a primer containing the sequence of SEQ ID NO: 128 and a primer containing the sequence of SEQ ID NO: 129; a pair of primers 7 represented by a primer containing the sequence of SEQ ID NO: 130 and a primer containing the sequence of SEQ ID NO: 131; a pair of primers 8 represented by a primer containing the sequence of SEQ ID NO: 132 and a primer containing the sequence of SEQ ID NO: 133; a pair of primers 9 represented by a primer containing the sequence of SEQ ID NO: 134 and a primer containing the sequence of SEQ ID NO: 135; a pair of primers 10 represented by a primer containing the sequence of SEQ ID NO: 136 and a primer containing the sequence of SEQ ID NO: 137; a pair of primers 11 represented by a primer containing the sequence of SEQ ID NO: 138 and a primer containing the sequence of SEQ ID NO: 139; a pair of primers 12 represented by a primer containing the sequence of SEQ ID NO: 140 and a primer containing the sequence of SEQ ID NO: 141; a pair of primers 13 represented by a primer containing the sequence of SEQ ID NO: 142 and a primer containing the sequence of SEQ ID NO: 143; a pair of primers 14 represented by a primer containing the sequence of SEQ ID NO: 144 and a primer containing the sequence of SEQ ID NO: 145; a pair of primers 15 represented by a primer containing the sequence of SEQ ID NO: 146 and a primer containing the sequence of SEQ ID NO: 147; a pair of primers 16 represented by a primer containing the sequence of SEQ ID NO: 148 and a primer containing the sequence of SEQ ID NO: 149; a pair of primers 17 represented by a primer containing the sequence of SEQ ID NO: 150 and a primer containing the sequence of SEQ ID NO: 151; a pair of primers 18 represented by a primer containing the sequence of SEQ ID NO: 152 and a primer containing the sequence of SEQ ID NO: 153; a pair of primers 19 represented by a primer containing the sequence of SEQ ID NO: 154 and a primer containing the sequence of SEQ ID NO: 155; a pair of primers 20 represented by a primer containing the sequence of SEQ ID NO: 156 and a primer containing the sequence of SEQ ID NO: 157; a pair of primers 21 represented by a primer containing the sequence of SEQ ID NO: 158 and a primer containing the sequence of SEQ ID NO: 159, a pair of primers 22 represented by a primer containing the sequence of SEQ ID NO: 160 and a primer containing the sequence of SEQ ID NO: 161; a pair of primers 23 represented by a primer containing the sequence of SEQ ID NO: 162, and a primer containing the sequence of SEQ ID NO: 163; a pair of primers 24 represented by a primer containing the sequence of SEQ ID NO: 164 and a primer containing the sequence of SEQ ID NO: 165; a pair of primers 25 represented by a primer containing the sequence of SEQ ID NO: 166 and a primer containing the sequence of SEQ ID NO: 167; a pair of primers 26, represented by a primer containing the sequence of SEQ ID NO: 168, and a primer containing the sequence of SEQ ID NO: 169; a pair of primers 27 represented by a primer containing the sequence of SEQ ID NO: 170 and a primer containing the sequence of SEQ ID NO: 171; a pair of primers 28 represented by a primer containing the sequence of SEQ ID NO: 172, and a primer containing the sequence of SEQ ID NO: 173, a pair of primers 29 represented by a primer containing the sequence of SEQ ID NO: 174, and a primer containing the sequence of SEQ ID NO: 175; a pair of primers 30 represented by a primer containing the sequence of SEQ ID NO: 176 and a primer containing the sequence of SEQ ID NO: 177; a pair of primers 31 represented by a primer containing the sequence of SEQ ID NO: 178 and a primer containing the sequence of SEQ ID NO: 179; a pair of primers 32 represented by a primer containing the sequence of SEQ ID NO: 180 and a primer containing the sequence of SEQ ID NO: 181; a pair of primers 33, represented by a primer containing the sequence of SEQ ID NO: 182, and a primer containing the sequence of SEQ ID NO: 183; a pair of primers 34 represented by a primer containing the sequence of SEQ ID NO: 184 and a primer containing the sequence of SEQ ID NO: 185; a pair of primers 35 represented by a primer containing the sequence of SEQ ID NO: 186 and a primer containing the sequence of SEQ ID NO: 187; a pair of primers 36 represented by a primer containing the sequence of SEQ ID NO: 188 and a primer containing the sequence of SEQ ID NO: 189; a pair of primers 37, represented by a primer containing the sequence of SEQ ID NO: 190, and a primer containing the sequence of SEQ ID NO: 191; a pair of primers 38 represented by a primer containing the sequence of SEQ ID NO: 192 and a primer containing the sequence of SEQ ID NO: 193; a pair of primers 39, represented by a primer containing the sequence of SEQ ID NO: 194, and a primer containing the sequence of SEQ ID NO: 195; a pair of primers 40 represented by a primer containing the sequence of SEQ ID NO: 196 and a primer containing the sequence of SEQ ID NO: 197; a pair of primers 41 represented by a primer containing the sequence of SEQ ID NO: 198 and a primer containing the sequence of SEQ ID NO: 199; a pair of primers 42 represented by a primer containing the sequence of SEQ ID NO: 200 and a primer containing the sequence of SEQ ID NO: 201; a pair of primers 43 represented by a primer containing the sequence of SEQ ID NO: 202 and a primer containing the sequence of SEQ ID NO: 203; a pair of primers 44 represented by a primer containing the sequence SEQ sequence SEQ ID NO: 204 and a primer containing the sequence SEQ ID NO: 205; a pair of primers 45 represented by a primer containing the sequence SEQ ID NO: 206 and a primer containing the sequence SEQ ID NO: 207; a pair of primers 46 represented by a primer containing the sequence of SEQ ID NO: 208 and a primer containing the sequence of SEQ ID NO: 209; a pair of primers 47 represented by a primer containing the sequence of SEQ ID NO: 210 and a primer containing the sequence of SEQ ID NO: 211; a pair of primers 48 represented by a primer containing the sequence of SEQ ID NO: 212 and a primer containing the sequence of SEQ ID NO: 213; a pair of primers 49 represented by a primer containing the sequence of SEQ ID NO: 214 and a primer containing the sequence of SEQ ID NO: 215; a pair of primers 50 represented by a primer containing the sequence of SEQ ID NO: 216 and a primer containing the sequence of SEQ ID NO: 217; a pair of primers 51 represented by a primer containing the sequence of SEQ ID NO: 218 and a primer containing the sequence of SEQ ID NO: 219; a pair of primers 52 represented by a primer containing the sequence of SEQ ID NO: 220, and a primer containing the sequence of SEQ ID NO: 221, a pair of primers 53 represented by a primer containing the sequence of SEQ ID NO: 222, and a primer containing the sequence of SEQ ID NO: 223; a pair of primers 54 represented by a primer containing the sequence of SEQ ID NO: 224, and a primer containing the sequence of SEQ ID NO: 225, a pair of primers 55 represented by a primer containing the sequence of SEQ ID NO: 226, and a primer containing the sequence of SEQ ID NO: 227; a pair of primers 56 represented by a primer containing the sequence of SEQ ID NO: 228 and a primer containing the sequence of SEQ ID NO: 229; and a pair of primers 57 represented by a primer containing the sequence of SEQ ID NO: 230, and a primer containing the sequence of SEQ ID NO: 231; and

(b) introgression of the allele of interest into the germinal plasma of Zea mays in which this allele is absent. In some embodiments of the invention, the allele of interest contains one of the sequences of SEQ ID NO: l-117, 400, 401 or a nucleotide sequence that is at least 85%, 90% or 95% identical along its entire length with one of sequences SEQ ID NO: l-117, 400 and 401. In some embodiments, the allele of interest is a favorable allele and / or a favorable haplotype that positively correlates with a sign of optimized water consumption.

In some embodiments, the favorable allele contains a nucleotide sequence at least 90% identical to one or more sequences of SEQ ID NOs: 1-117, 400 and 401, and further comprises one or more specific nucleotides and combinations of the positions disclosed herein. By way of example, but not limitation, in some embodiments, the favorable allele contains a nucleotide sequence that is at least 90% identical:

SEQ ID NO: 1, and further comprises a nucleotide G at a position that corresponds to position 115 of the sequence SEQ ID NO: 1, nucleotide A at a position that corresponds to position 270 of the sequence SEQ ID NO: 1, nucleotide T at a position that corresponds to position 301 the sequence of SEQ ID NO: 1, nucleotide A at the position that corresponds to position 483 of the sequence SEQ ID NO: 1, or any combination thereof;

SEQ ID NO: 2, and further comprises a nucleotide G at a position that corresponds to position 100 and a deletion at a position that corresponds to position 264-271 of the sequence SEQ ID NO: 2, or a combination thereof;

SEQ ID NO: 3, and further comprises a nucleotide G at a position that corresponds to position 216 of the sequence SEQ ID NO: 3;

SEQ ID NO: 4, and further comprises nucleotide A at a position that corresponds to position 503 of the sequence SEQ ID NO: 4;

SEQ ID NO: 5, and further comprises a CGCG tetranucleotide at a position that corresponds to position 818-821 of the sequence SEQ ID NO: 5;

SEQ ID NO: 6, and further comprises a nucleotide G or A at a position that corresponds to position 254 of the sequence SEQ ID NO: 6;

SEQ ID NO: 7, and further comprises a GA dinucleotide at a position that corresponds to positions 4497-4498 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide C or T at a position which corresponds to position 4792 of the sequence SEQ ID NO: 7, nucleotide T at the position which corresponds to position 4836 of the sequence SEQ ID NO: 7, trinucleotide ACT or TCC at the position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7 or any combination thereof ; or additionally contains a deletion at positions 4497-4498 of SEQ ID NO: 7, nucleotide G at a position that corresponds to position 4505 of SEQ ID NO: 7, nucleotide T at a position that corresponds to position 4609 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide T at a position that corresponds to position 4792 of the sequence SEQ ID NO: 7, nucleotide T at a position that corresponds to position 4836 of the sequence SEQ ID NO: 7, nucleotide C at position which corresponds to 4844 ozitsii sequence SEQ ID NO: 7, a nucleotide G at a position which corresponds to position 4969 sequence SEQ ID NO: 7 and TCC trinucleotide in a position which corresponds to positions 4979-4981 sequence of SEQ ID NO: 7;

SEQ ID NO: 8, and further comprises nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 8 and optionally further comprises nucleotide G at a position that corresponds to position 390 of SEQ ID NO: 8 and nucleotide A at which corresponds to position 477 of the sequence SEQ ID NO: 8, or any combination thereof;

SEQ ID NO: 9, and further comprises nucleotide C at a position that corresponds to position 292 of the sequence SEQ ID NO: 9;

SEQ ID NO: 10, and further comprises nucleotide A at a position that corresponds to position 166 of the sequence SEQ ID NO: 10;

SEQ ID NO: 11, and further comprises a nucleotide G at a position that corresponds to position 148 of the sequence SEQ ID NO: 11;

SEQ ID NO: 12, and further comprises nucleotide C at a position that corresponds to position 94 of the sequence of SEQ ID NO: 12;

SEQ ID NO: 13, and further comprises nucleotide A at a position that corresponds to position 35 of the sequence SEQ ID NO: 13, nucleotide C at a position that corresponds to position 148 of the sequence SEQ ID NO: 1; 3 or nucleotide G at a position that corresponds to position 89 of the sequence SEQ ID NO: 13, or any combination thereof;

SEQ ID NO: 14, and further comprises a nucleotide G at a position that corresponds to position 432 of the sequence SEQ ID NO: 14;

SEQ ID NO: 15, and further comprises nucleotide A at a position that corresponds to position 753 of the sequence SEQ ID NO: 15;

SEQ ID NO: 16, and further comprises a nucleotide G at a position that corresponds to position 755 of the sequence SEQ ID NO: 16;

SEQ ID NO: 17, and further comprises a nucleotide G at a position that corresponds to position 431 of the sequence SEQ ID NO: 17;

SEQ ID NO: 18 and further comprises a nucleotide G or T at a position that corresponds to position 518 of the sequence SEQ ID NO: 18;

SEQ ID NO: 19, and further comprises nucleotide A at a position that corresponds to position 182 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, or nucleotide G or C at a position that corresponds to position 463 of the sequence SEQ ID NO: 19, or any combination thereof, or a sequence that further comprises a nucleotide G at a position that corresponds to position 182 of the sequence SEQ ID N0: 19, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19 : 19, well cleotide G at a position that corresponds to position 330 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19;

SEQ ID NO: 20, and further comprises a CTGG tetranucleotide at a position that corresponds to positions 773-776 of the sequence SEQ ID NO: 20;

SEQ ID NO: 21, and further comprises a nucleotide deletion at positions that correspond to positions 316-324 of SEQ ID NO: 21, or a sequence that further comprises nucleotide C at a position that corresponds to position 61 of SEQ ID NO: 21, nucleotide C at a position that corresponds to position 200 of the sequence SEQ ID NO: 21 and a deletion at a position that corresponds to positions 316-324 of the sequence SEQ ID NO: 21;

SEQ ID NO: 22, and further comprises a nucleotide G at a position that corresponds to position 211 of the sequence SEQ ID NO: 22,

SEQ ID NO: 23, and further comprises a nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 23, or a combination thereof;

SEQ ID NO: 24, and further comprises nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24;

SEQ ID NO: 25, and further comprises a nucleotide G at a position that corresponds to position 562 of the sequence SEQ ID NO: 25;

SEQ ID NO: 26, and further comprises nucleotide C at a position that corresponds to position 1271 of the sequence SEQ ID NO: 26;

SEQ ID NO: 27, and further comprises a nucleotide C or T at a position that corresponds to position 254 of the sequence SEQ ID NO: 27, or which optionally further comprises a nucleotide G at a position that corresponds to position 64 of the sequence SEQ ID NO 27 and nucleotide T at the position that corresponds to position 254 of the sequence SEQ ID NO: 27;

SEQ ID NO: 28, and further comprises a nucleotide T at a position that corresponds to position 496 of the sequence SEQ ID NO: 28; or additionally contains nucleotide C at a position that corresponds to position 98 of the sequence SEQ ID NO: 28, nucleotide T at the position that corresponds to position 147 of the sequence SEQ ID NO: 28, nucleotide C at the position that corresponds to position 224 of the sequence SEQ ID NO: 28 and nucleotide T at a position that corresponds to position 496 of the sequence SEQ ID NO: 28;

SEQ ID NO: 29, and further comprises nucleotide C at a position that corresponds to position 258 of the sequence SEQ ID NO: 29;

SEQ ID NO: 30, and further comprises a nucleotide T at a position that corresponds to position 259 of the sequence SEQ ID NO: 30, a nucleotide G at a position that corresponds to position 398 of the sequence SEQ ID NO: 30 or a combination thereof; or which contains a nucleotide T at a position that corresponds to position 259 of the sequence SEQ ID NO: 30, a nucleotide T at a position that corresponds to position 296 of the sequence SEQ ID NO: 30, nucleotide A at a position that corresponds to position 398 of the sequence SEQ ID NO: 30 and nucleotide C at the position that corresponds to position 1057 of the sequence of SEQ ID NO: 30;

SEQ ID NO: 31, and further comprises a nucleotide G at a position that corresponds to position 239 of the sequence SEQ ID NO: 31;

SEQ ID NO: 32, and further comprises a nucleotide G at a position that corresponds to position 208 of the sequence SEQ ID NO: 32;

SEQ ID NO: 33, and further comprises nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33;

SEQ ID NO: 34, and further comprises a CA dinucleotide at a position that corresponds to position 144-145 of SEQ ID NO: 34, a nucleotide T at a position that corresponds to position 169 of SEQ ID NO: 34, nucleotide A at a position that corresponds position 537 of the sequence SEQ ID NO: 34, or any combination thereof;

SEQ ID NO: 35, and further comprises a nucleotide G at a position that corresponds to position 76 of the sequence of SEQ ID NO: 35;

SEQ ID NO: 36, and further comprises a nucleotide T at a position that corresponds to position 698 of the sequence SEQ ID NO: 36; or which contains nucleotide C at a position that corresponds to position 500 of the sequence SEQ ID NO: 36, nucleotide G at the position that corresponds to position 568 of the sequence SEQ ID NO: 36 and nucleotide T at the position that corresponds to position 698 of the sequence SEQ ID NO: 36 ;

SEQ ID NO: 37, and further comprises nucleotide A at a position that corresponds to position 375 of the sequence SEQ ID NO: 37, nucleotide A or G at the position that corresponds to position 386 of the sequence SEQ ID NO: 37, or a combination thereof;

SEQ ID NO: 38, and further comprises nucleotide C at a position that corresponds to position 309 of the sequence SEQ ID NO: 38, nucleotide A at the position that corresponds to position 342 of the sequence SEQ ID NO: 38, or a combination thereof;

SEQ ID NO: 39, and further comprises a nucleotide G or C at a position that corresponds to position 445 of the sequence SEQ ID NO: 39;

SEQ ID NO: 40, and further comprises nucleotide A at a position that corresponds to position 602 of the sequence SEQ ID NO: 40;

SEQ ID NO: 41, and further comprises a nucleotide G or A at a position that corresponds to position 190 of the sequence SEQ ID NO: 41, nucleotide C at a position that corresponds to position 580 of the sequence SEQ ID NO: 41, or a combination thereof;

SEQ ID NO: 42, and further comprises a TSH trinucleotide at a position that corresponds to positions 266-268 of SEQ ID NO: 42, or which further comprises a nucleotide A at a position that corresponds to position 238 of SEQ ID NO: 42, a nucleotide deletion, which corresponds to positions 266-268 of the sequence SEQ ID NO: 42, and nucleotide C at the position which corresponds to position 808 of the sequence SEQ ID NO: 42;

SEQ ID NO: 43, and further comprises nucleotide C or A at a position that corresponds to position 708 of the sequence SEQ ID NO: 43;

SEQ ID NO: 44, and further comprises nucleotide A at a position that corresponds to position 266 of the sequence SEQ ID NO: 44;

SEQ ID NO: 45, and further comprises a nucleotide T at a position that corresponds to position 475 of the sequence SEQ ID NO: 45;

SEQ ID NO: 46, and further comprises nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

SEQ ID NO: 47, and further comprises a nucleotide G at a position that corresponds to position 87 of the sequence SEQ ID NO: 47;

SEQ ID NO: 48, and further comprises nucleotide A or G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48;

SEQ ID NO: 49, and further comprises nucleotide G at a position that corresponds to position 650 of the sequence SEQ ID NO: 49 and optionally further further comprises nucleotide C at a position that corresponds to position 166 of SEQ ID NO: 49 and nucleotide A at which corresponds to position 224 of the sequence SEQ ID NO: 49, and nucleotide G at the position which corresponds to position 892 of the sequence SEQ ID NO: 49;

SEQ ID NO: 50, and further comprises a nucleotide T or A at a position that corresponds to position 541 of the sequence SEQ ID NO: 50;

SEQ ID NO: 51, and further comprises a nucleotide G at a position that corresponds to position 111 of the sequence SEQ ID NO: 51;

SEQ ID NO: 52 and further comprises a nucleotide C or G at a position that corresponds to position 442 of the sequence SEQ ID NO: 52;

SEQ ID NO: 53 and further comprises nucleotide C or T at a position that corresponds to position 428 of the sequence SEQ ID NO: 53, nucleotide C at the position that corresponds to position 491 of the sequence SEQ ID NO: 53, or a combination thereof; or which further comprises nucleotide C at positions that correspond to positions 83,428,491 and 548 of the sequence SEQ ID NO: 53;

SEQ ID NO: 54, and further comprises nucleotide A at a position that corresponds to position 126 of the sequence SEQ ID NO: 54;

SEQ ID NO: 55, and further comprises a nucleotide G at a position that corresponds to position 193 of the sequence SEQ IDNO: 55;

SEQ ID NO: 56, and further comprises nucleotide A or G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide C at a position that corresponds to position 516 of the sequence SEQ ID NO: 56, or a combination thereof;

SEQ ID NO: 57 and further comprises a nucleotide T at a position that corresponds to position 173 of the sequence SEQ ID NO: 57;

SEQ ID NO: 58, and further comprises nucleotide C at a position that corresponds to position 486 of the sequence SEQ ID NO: 58;

SEQ ID NO: 59 and further comprises a nucleotide G at a position that corresponds to position 729 of the sequence SEQ ID NO: 59; and / or

SEQ ID NO: 60 and further comprises a nucleotide G at a position that corresponds to position 267 of the sequence SEQ ID NO: 60.

Methods for producing a drought tolerant corn plant may comprise detecting in a germplasm a marker associated with increased drought tolerance and producing a corn plant from said germplasm. Germplasm may be a non-naturally occurring variety of corn. In some embodiments, the germplasm gene is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of an elite variety of corn. In some embodiments, the germplasm gene is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of NP2391.

In some embodiments, alleles containing a marker associated with increased drought tolerance are detected using a variety of probes selected from the group consisting of:

1) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 100, SEQ ID NO: 104 and SEQ ID NO: 109;

2) a haplotype containing the sequences of SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 93, SEQ ID NO: 102, SEQ ID NO: 106, SEQ ID NO: 110 and SEQ ID NO: 111;

3) a haplotype containing the sequences of SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 93, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 104, SEQ ID NO: 105 and SEQ ID NO: 112;

4) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 97, SEQ ID NO: 102, SEQ ID NO: 103 and SEQ ID NO: 105;

5) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 97, SEQ ID NO: 101 SEQ ID NO: 107, SEQ ID NO: 108 SEQ ID NO: 109 and SEQ ID NO: 112; and

6) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 91, SEQ ID NO: 98, SEQ ID NO: 101 and SEQ ID NO: 112.

In some embodiments, alleles containing a marker associated with increased drought tolerance are detected using a variety of probes selected from the group consisting of:

1) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 89 and SEQ ID NO: 95;

2) a haplotype containing the sequences of SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 93, SEQ ID NO: 102 and SEQ ID NO: 106;

3) a haplotype containing the sequences of SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 93, SEQ ID NO: 98 and SEQ ID NO: 112;

4) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 93 and SEQ ID NO: 102;

5) a haplotype containing the sequences of SEQ ID NO: 87, SEQ ID NO: 94, SEQ ID NO: 101 and SEQ ID NO: 112; and

6) a haplotype containing the sequences of SEQ ID NO: 88, SEQ ID NO: 98, SEQ ID NO: 101 and SEQ ID NO: 112.

In some embodiments of the invention, the allele (s) containing the marker associated with increased drought tolerance is detected using a probe or probes selected from the group consisting of:

1) the sequence of SEQ ID NO: 87;

2) the sequence of SEQ ID NO: 88;

3) a haplotype containing the sequences of SEQ ID NO: 86 and SEQ ID NO: 87; and

4) a haplotype containing the sequences of SEQ ID NO: 88 and SEQ ID NO: 90. In some embodiments, alleles containing a marker associated with increased drought tolerance are found in amplification products from a nucleic acid sample isolated from a corn plant or germplasm, moreover, the amplification products are produced using pairs of amplification primers selected from the group consisting of the sequences:

1) SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 33 and SEQ ID NO: 61, SEQ ID NO: 35 and SEQ ID NO: 63, SEQ ID NO: 39 and SEQ ID NO: 67, SEQ ID NO: 41 and SEQ ID NO: 69, SEQ ID NO: 44 and SEQ ID NO: 72, SEQ ID NO: 48 and SEQ ID NO: 76 and SEQ ID NO: 53 and SEQ ID NO: 81;

2) SEQ ID NO: 30 and SEQ ID NO: 58, SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 33 and SEQ ID NO: 61, SEQ ID NO: 37 and SEQ ID NO: 65, SEQ ID NO: 46 and SEQ ID NO: 74, SEQ ID NO: 50 SEQ ID NO: 78, SEQ ID NO: 54 and SEQ ID NO: 82, SEQ ID NO: 55 and SEQ ID NO: 83;

3) SEQ ID NO: 29 and SEQ ID NO: 57, SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 34 and SEQ ID NO: 62, SEQ ID NO: 37 and SEQ ID NO: 65, SEQ ID NO: 40 and SEQ ID NO: 68, SEQ ID NO: 42 and SEQ ID NO: 70, SEQ ID NO: 43 and SEQ ID NO: 71, SEQ ID NO: 48 and SEQ ID NO: 76, SEQ ID NO: 49 and SEQ ID NO: 77 and SEQ ID NO: 56 and SEQ ID NO: 84;

4) SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 35 and SEQ ID NO: 63, SEQ ID NO: 37 and SEQ ID NO: 65, SEQ ID NO: 41 and SEQ ID NO: 69, SEQ ID NO: 46 and SEQ ID NO: 74, SEQ ID NO: 47 and SEQ ID NO: 75 and SEQ ID NO: 49 and SEQ ID NO: 77;

5) SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 36 and SEQ ID NO: 64, SEQ ID NO: 38 and SEQ ID NO: 66, SEQ ID NO: 41 and SEQ ID NO: 69, SEQ ID NO: 45 and SEQ ID NO: 73, SEQ ID NO: 51 and SEQ ID NO: 79, SEQ ID NO: 52 and SEQ ID NO: 80, SEQ ID NO: 53 and SEQ ID NO: 81 and SEQ ID NO: 56 and SEQ ID NO: 84 and

6) SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 35 and SEQ ID NO: 63, SEQ ID NO: 42 and SEQ ID NO: 70, SEQ ID NO: 45 and SEQ ID NO: 73 and SEQ ID NO: 56 and SEQ ID NO: 84.

In some embodiments of the invention, alleles containing a marker associated with increased drought tolerance are detected in amplification products from a nucleic acid sample isolated from a corn plant or germplasm, the amplification products being produced using pairs of amplification primers selected from the group consisting of:

1) SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 33 and SEQ ID NO: 61, and SEQ ID NO: 39 and SEQ ID NO: 67;

2) SEQ ID NO: 30 and SEQ ID NO: 58, SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 33 and SEQ ID NO: 61, SEQ ID NO: 37 and SEQ ID NO: 65, SEQ ID NO: 46 and SEQ ID NO: 74 and SEQ ID NO: 50 and SEQ ID NO: 78;

3) SEQ ID NO: 29 and SEQ ID NO: 57, SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 34 and SEQ ID NO: 62, SEQ ID NO: 37 and SEQ ID NO: 65, SEQ ID NO: 42 and SEQ ID NO: 70 and SEQ ID NO: 56 and SEQ ID NO: 84,

4) SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 37 and SEQ ID NO: 65 and SEQ ID NO: 46 and SEQ ID NO: 74;

5) SEQ ID NO: 31 and SEQ ID NO: 59, SEQ ID NO: 38 and SEQ ID NO: 66, SEQ ID NO: 45 and SEQ ID NO: 73 and SEQ ID NO: 56 and SEQ ID NO: 84; and

6) SEQ ID NO: 32 and SEQ ID NO: 60, SEQ ID NO: 42 and SEQ ID NO: 70, SEQ ID NO: 45 and SEQ ID NO: 73 and SEQ ID NO: 56 and SEQ ID NO: 84.

In some embodiments of the invention, the allele (s) containing the marker associated with increased drought tolerance is detected in the amplification product or products from a nucleic acid sample isolated from a corn plant or germplasm, the amplification products being produced using amplification primer pairs selected from the group consisting of sequences:

1) SEQ ID NO: 31 and SEQ ID NO: 59;

2) SEQ ID NO: 32 and SEQ ID NO: 60;

3) SEQ ID NO: 30 and SEQ ID NO: 58 and SEQ ID NO: 31 and SEQ ID NO: 59; and

4) SEQ ID NO: 32 and SEQ ID NO: 60 and SEQ ID NO: 34 and SEQ ID NO: 62.

Methods for introgression of an allele associated with increased drought tolerance into a corn plant or germplasm may include crossing the first corn plant or germplasm containing said allele (donor) with a second corn plant or germplasm that does not have said allele (recurrent parent) and re-crossing the offspring containing the said allele with a recurrent parent. Descendants containing the said allele can be identified by detecting in their genomes the presence of a marker associated with increased drought tolerance. Either the donor or the recurrent parent, or both, may be an unnatural corn variety. In some embodiments, the donor is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno YEN 692. In some embodiments, the donor gene is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments of the invention the recurrent parent is an elite variety of corn. In some embodiments, the recurrent parent genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of an elite variety of corn. In some embodiments, the recurrent parent is NP2391. In some embodiments, the recurrent parent genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of NP2391.

In some embodiments, an object of the invention disclosed herein also relates to methods for producing a drought tolerant corn plant. In some embodiments of the invention, the methods disclosed herein comprise detecting in corn germplasm the presence of a marker associated with increased drought tolerance, said marker being selected from the group consisting of:

nucleotide G at a position that corresponds to position 100 of the sequence SEQ ID NO: 2, trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, nucleotide A at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide T in position cat paradise corresponds to position 173 sequence SEQ ID N0: 57 and the nucleotide G at a position which corresponds to position 267 sequence SEQ ID NO: 60;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 562 of the sequence SEQ ID NO: 25, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at the position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A in position to which corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position which corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide G at a position that corresponds to position 100, nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 217 of SEQ ID NO: 23, nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide G at the position that corresponds to position 472 of the last successive SEQ ID NO: 48, a nucleotide G at a position which corresponds to position 193 sequence SEQ ID NO: 55 and the nucleotide C at a position which corresponds to position 486 sequence SEQ ID NO: 58;

a nucleotide deletion at a position that corresponds to positions 264-271 of SEQ ID NO: 2, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, and nucleotide C at the position that corresponds to position 486 of the sequence SEQ ID NO: 58;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 254 of the sequence SEQ ID NO: 27, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, nucleotide G at the position that corresponds to position 193 of the sequence SEQ ID NO: 55, nucleotide C in position cat the original corresponds to position 516 of the sequence SEQ ID NO: 56, nucleotide G at the position that corresponds to position 729 of the sequence SEQ ID NO: 59, and nucleotide G at the position that corresponds to position 267 of the sequence SEQ ID NO: 60;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55, and a nucleotide G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 472 of SEQ ID NO: 48, nucleotide A at a position that corresponds to position 237 of SEQ ID NO: 56, and nucleotide T at a position which corresponds to position 173 of the sequence SEQ ID NO: 57;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position that corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at the position that corresponds to position 87 of the sequence SEQ ID NO: 47, nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48, and a nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide A at a position that corresponds to position 309 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, and nucleotide G at a position which corresponds to position 193 of the sequence SEQ ID NO: 55;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7;

nucleotide A at a position that corresponds to position 4641 of the sequence of SEQ ID NO: 7;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, and nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, and nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48,

and combinations thereof, as well as

producing a plant from said corn germplasm, thereby producing a drought tolerant corn plant.

The subject matter disclosed herein also relates to methods for detecting and / or breeding a drought tolerant corn plant or germplasm. Methods for selection of a drought tolerant corn plant or germplasm may comprise crossing a first corn plant or germplasm with a second corn plant or germplasm, said first corn plant or germplasm containing a marker associated with increased drought tolerance and breeding a descendant plant or germ containing said marker associated with increased drought tolerance. The first or second corn plant or germplasm, or both the corn plant and germplasm may be an unnatural corn variety. In some embodiments, the first corn plant or germplasm is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, the genome of the first corn plant or germplasm is at least about 50% , 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments, the second corn plant or germplasm is an elite variety of corn. In some embodiments, the genome of the second corn plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97% , 99% or 100% identical to that of the elite variety of corn. In some embodiments, the second corn plant or germplasm is a variety of NP2391. In some embodiments, the genome of the second corn plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97% , 99% or 100% identical to that of NP2391.

Thus, in some embodiments of the invention, the methods comprise detecting a marker associated with increased drought tolerance in said corn plant or germplasm, said marker containing a plurality of alleles that are detected in amplification products from a nucleic acid sample isolated from said corn plant or germinal plasma, and said amplification products were produced using pairs of amplification primers selected from uppy consisting of:

(I) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 160 and 161; SEQ ID NO: 180 and 181; SEQ ID NO: 208 and 209; SEQ ID NO: 222 and 223; SEQ ID NO: 224 and 225; and SEQ ID NO: 230 and 231;

(II) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 164 and 165; SEQ ID NO: 166 and 167; SEQ ID NO: 202 and 203; SEQ ID NO: 204 and 205; SEQ ID NO: 208 and 209; and SEQ ID NO: 212 and 213;

(III) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 160 and 161; SEQ ID NO: 162 and 163; SEQ ID NO: 172 and 173; SEQ ID NO: 202 and 203; SEQ ID NO: 206 and 207; SEQ ID NO: 208 and 209; SEQ ID NO: 220 and 221; and SEQ ID NO: 226 and 227;

(IV) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 180 and 181; SEQ ID NO: 202 and 203; SEQ ID NO: 222 and 223; and SEQ ID NO: 226 and 227;

(V) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 168 and 169; SEQ ID NO: 180 and 181; SEQ ID NO: 202 and 203; SEQ ID NO: 220 and 221; SEQ ID NO: 222; and 223; SEQ ID NO: 228 and 229; and SEQ ID NO: 230 and 231;

(VI) SEQ IDNO: 130 and 131; SEQ IDNO: 152 and 153; SEQ IDNO: 172 and 173; SEQ IDNO: 220 and 221; and SEQ ID NO: 222 and 223;

(VII) SEQ ID NO: 130 and 131; SEQ ID NO: 208 and 209; SEQ ID NO: 222; and 223 and SEQ ID NO: 224 and 225;

(VIII) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 166 and 167; SEQ ID NO: 202 and 203; SEQ ID NO: 204 and 205; SEQ ID NO: 208 and 209; and SEQ ID NO: 212 and 213;

(IX) SEQ ID NO: 130 and 131; SEQ ID NO: 172 and 173; SEQ ID NO: 202 and 203; SEQ ID NO: 206 and 207; SEQ ID NO: 208 and 209; and SEQ ID NO: 220 and 221;

(X) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 202 and 203; and SEQ ID NO: 222 and 223;

(XI) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 202 and 203; and SEQ ID NO: 220 and 221;

(XII) SEQ ID NO: 130 and 131;

(XIII) SEQ ID NO: 130 and 131; and SEQ ID NO: 204 and 205; and

(XIV) SEQ ID NO: 130 and 131; and SEQ ID NO: 208 and 209,

thus identifying and / or selecting a drought tolerant corn plant or germplasm.

The subject matter disclosed herein also relates to methods for producing a drought tolerant corn plant, comprising detecting a marker associated with increased drought tolerance in the corn germplasm, said marker containing a plurality of alleles that are detected in amplification products from a nucleic acid sample isolated from said corn plants or germplasm, wherein said amplification product was produced using steam Reimer amplification selected from the group consisting of:

(I) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 160 and 161; SEQ ID NO: 180 and 181; SEQ ID NO: 208 and 209; SEQ ID NO: 222 and 223; SEQ ID NO: 224 and 225; and SEQ ID NO: 230 and 231;

(II) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 164 and 165; SEQ ID NO: 166 and 167; SEQ ID NO: 202 and 203; SEQ ID NO: 204 and 205; SEQ ID NO: 208 and 209; and SEQ ID NO: 212 and 213;

(III) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 160 and 161; SEQ ID NO: 162 and 163; SEQ ID NO: 172 and 173; SEQ ID NO: 202 and 203; SEQ ID NO: 206 and 207; SEQ ID NO: 208 and 209; SEQ ID NO: 220 and 221; and SEQ ID NO: 226 and 227;

(IV) SEQ ID NO: 120 and 121; SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 180 and 181; SEQ ID NO: 202 and 203; SEQ ID NO: 222 and 223; and SEQ ID NO: 226 and 227;

(V) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 168 and 169; SEQ ID NO: 180 and 181; SEQ ID NO: 202 and 203; SEQ ID NO: 220 and 221; SEQ ID NO: 222 and 223; SEQ ID NO: 228 and 229; and SEQ ID NO: 230 and 231;

(VI) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 172 and 173; SEQ ID NO: 220 and 221; and SEQ ID NO: 222 and 223;

(VII) SEQ ID NO: 130 and 131; SEQ ID NO: 208 and 209; SEQ ID NO: 222 and 223; and SEQ ID NO: 224 and 225;

(VIII) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 166 and 167; SEQ ID NO: 202 and 203; SEQ ID NO: 204 and 205; SEQ ID NO: 208 and 209; and SEQ ID NO: 212 and 213;

(IX) SEQ ID NO: 130 and 131; SEQ ID NO: 172 and 173; SEQ ID NO: 202 and 203; SEQ ID NO: 206 and 207; SEQ ID NO: 208 and 209; and SEQ ID NO: 220 221;

(X) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 202 and 203; and SEQ ID NO: 222 and 223;

(XI) SEQ ID NO: 130 and 131; SEQ ID NO: 152 and 153; SEQ ID NO: 202 and 203; and SEQ ID NO: 220 and 221;

(XII) SEQ ID NO: 130 and 131;

(XIII) SEQ ID NO: 130 and 131; and SEQ ID NO: 204 and 205; and

(XIV) SEQ ID NO: 130 and 131; and SEQ ID NO: 208 and 209 and

producing a plant from said corn germplasm, thereby producing a drought tolerant corn plant.

The subject matter disclosed herein also relates to methods for detecting and / or breeding a drought tolerant corn plant or germplasm comprising detecting in the said corn plant or germplasm the presence of a marker associated with increased drought tolerance, said marker containing a plurality of alleles that are detected by a plurality of probes selected from the group consisting of:

(I) SEQ ID NO: 348 and 349; SEQ ID NO: 350 and 351; SEQ ID NO: 360 and 361; SEQ ID NO: 372 and 373; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; SEQ ID NO: 382 and 383; and SEQ ID NO: 398 and 399;

(II) SEQ ID NO: 350 and 251; SEQ ID NO: 356 and 357; SEQ ID NO: 364 and 365; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(III) SEQ ID NO: 348 and 349; SEQ ID NO: 352 and 353; SEQ ID NO: 358 and 359; SEQ ID NO: 362 and 363; SEQ ID NO: 370 and 371; SEQ ID NO: 374 and 375; SEQ ID NO: 382 and 383; SEQ ID NO: 386 and 387; and SEQ ID NO: 394 and 395;

(IV) SEQ ID NO: 346 and 347; SEQ ID NO: 352 and 353; SEQ ID NO: 356 and 357; SEQ ID NO: 372 and 373; SEQ ID NO: 388 and 389; and SEQ ID NO: 394 395;

(V) SEQ ID NO: 351 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 368 and 369; SEQ ID NO: 372 and 373; SEQ ID NO: 376 and 377; SEQ ID NO: 386 and 387; SEQ ID NO: 390 and 391; SEQ ID NO: 396 and 397; and SEQ ID NO: 398 and 399;

(VI) SEQ ID NO: 352 and 353; SEQ ID NO: 354 and 355; SEQ ID NO: 370 and 371; SEQ ID NO: 386 and 387; SEQ ID NO: 388 and 389;

(VII) SEQ ID NO: 350 and 351; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; and SEQ ID NO: 392 and 393;

(VIII) SEQ ID NO: 350 and 351; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(IX) SEQ ID NO: 352 and 353; SEQ ID NO: 370 and 371; SEQ ID NO: 380 and 381; SEQ ID NO: 382 and 383; and SEQ ID NO: 386 and 387;

(X) SEQ ID NO: 352 and 353; SEQ ID NO: 356; and 357; and SEQ ID NO: 388 and 389;

(XI) SEQ ID NO: 350 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 376 and 377; and SEQ ID NO: 386 and 387;

(XII) SEQ ID NO: 350 and 351;

(XIII) SEQ ID NO: 352 and 353;

(XIV) SEQ ID NO: 350 and 351; and SEQ ID NO: 378 and 379 and

(XV) SEQ ID NO: 352 and 353; and SEQ ID NO: 382 and 383,

thus identifying and / or selecting a drought tolerant corn plant or germplasm.

The object of the invention disclosed herein also relates to methods for producing a drought tolerant corn plant comprising detecting in a germinal germ plasma the presence of a marker associated with increased drought tolerance, said marker containing a plurality of alleles that are detected by a plurality of probes selected from the group consisting of:

(I) SEQ ID NO: 348 and 349; SEQ ID NO: 350 and 351; SEQ ID NO: 360 and 361; SEQ ID NO: 372 and 373; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; SEQ ID NO: 382 and 383; and SEQ ID NO: 398 and 399;

(II) SEQ ID NO: 350 and 251; SEQ ID NO: 356 and 357; SEQ ID NO: 364 and 365; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(III) SEQ ID NO: 348 and 349; SEQ ID NO: 352 and 353; SEQ ID NO: 358 and 359; SEQ ID NO: 362 and 363; SEQ ID NO: 370 and 371; SEQ ID NO: 374 and 375; SEQ ID NO: 382 and 383; SEQ ID NO: 386 and 387; and SEQ ID NO: 394 and 395;

(IV) SEQ ID NO: 346 and 347; SEQ ID NO: 352 and 353; SEQ ID NO: 356 and 357; SEQ ID NO: 372 and 373; SEQ ID NO: 388 and 389; and SEQ ID NO: 394 395;

(V) SEQ ID NO: 351 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 368 and 369; SEQ ID NO: 372 and 373; SEQ ID NO: 376 and 377; SEQ ID NO: 386 and 387; SEQ ID NO: 390 and 391; SEQ ID NO: 396 and 397; and SEQ ID NO: 398 and 399;

(VI) SEQ ID NO: 352 and 353; SEQ ID NO: 354 and 355; SEQ ID NO: 370 and 371; SEQ ID NO: 386 and 387; SEQ ID NO: 388 and 389;

(VII) SEQ ID NO: 350 and 351; SEQ ID NO: 382 and 383; SEQ ID NO: 388 and 389; and SEQ ID NO: 392 and 393;

(VIII) SEQ ID NO: 350 and 351; SEQ ID NO: 366 and 367; SEQ ID NO: 374 and 375; SEQ ID NO: 378 and 379; SEQ ID NO: 382 and 383; and SEQ ID NO: 384 and 385;

(IX) SEQ ID NO: 352 and 353; SEQ ID NO: 370 and 371; SEQ ID NO: 380 and 381; SEQ ID NO: 382 and 383; and SEQ ID NO: 386 and 387;

(X) SEQ ID NO: 352 and 353; SEQ ID NO: 356; and 357; and SEQ ID NO: 388 and 389;

(XI) SEQ ID NO: 350 and 351; SEQ ID NO: 354 and 355; SEQ ID NO: 376 and 377; and SEQ ID NO: 386 and 387;

(XII) SEQ ID NO: 350 and 351;

(XIII) SEQ ID NO: 352 and 353;

(XIV) SEQ ID NO: 350 and 351; and SEQ ID NO: 378 and 379 and

(XV) SEQ ID NO: 352 and 353; and SEQ ID NO: 382 and 383, and

producing a plant from said corn germplasm, thereby producing a drought tolerant corn plant. In some embodiments of the methods disclosed herein, a corn plant or germplasm is a non-naturally occurring variety of corn. In some embodiments, the genome of said corn plant or germplasm is at least 95% identical to that of NP2391.

The subject matter disclosed herein also relates, in some embodiments, to methods for selecting a drought tolerant corn plant or germplasm. In some embodiments of the invention, the methods comprise crossing a first corn plant or germplasm with a second corn plant or germplasm, said first corn plant or germplasm containing a haplotype associated with increased drought tolerance in its genome, said haplotype being selected from the group consisting of :

nucleotide G at a position that corresponds to position 100 of the sequence SEQ ID NO: 2, trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, nucleotide A at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide T in position cat paradise corresponds to position 173 sequence SEQ ID NO: 57 and the nucleotide G at a position which corresponds to position 267 sequence SEQ ID NO: 60;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 562 of the sequence SEQ ID NO: 25, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at the position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A in position to which corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position which corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide G at a position that corresponds to position 100, nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 217 of SEQ ID NO: 23, nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide G at the position that corresponds to position 472 of the last successive SEQ ID NO: 48, a nucleotide G at a position which corresponds to position 193 sequence SEQ ID NO: 55 and the nucleotide C at a position which corresponds to position 486 sequence SEQ ID NO: 58;

a nucleotide deletion at a position that corresponds to positions 264-271 of SEQ ID NO: 2, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, and nucleotide C at the position that corresponds to position 486 of the sequence SEQ ID NO: 58;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 254 of the sequence SEQ ID NO: 27, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, nucleotide G at the position that corresponds to position 193 of the sequence SEQ ID NO: 55, nucleotide C in position cat the original corresponds to position 516 of the sequence SEQ ID NO: 56, nucleotide G at the position that corresponds to position 729 of the sequence SEQ ID NO: 59, and nucleotide G at the position that corresponds to position 267 of the sequence SEQ ID NO: 60;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55, and a nucleotide G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 472 of SEQ ID NO: 48, nucleotide A at a position that corresponds to position 237 of SEQ ID NO: 56, and nucleotide T at a position which corresponds to position 173 of the sequence SEQ ID NO: 57;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position that corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at the position that corresponds to position 87 of the sequence SEQ ID NO: 47, nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48, and a nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide A at a position that corresponds to position 309 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, and nucleotide G at a position which corresponds to position 193 of the sequence SEQ ID NO: 55;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7;

nucleotide A at a position that corresponds to position 4641 of the sequence of SEQ ID NO: 7;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, and nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, and nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48,

and combinations thereof, as well as

selection of a descendant plant or germplasm that has the mentioned haplotype in its genome, thereby selecting a drought tolerant corn plant or germplasm. In some embodiments, either the first corn plant or germplasm or the second corn plant or germplasm, or both, is an unnatural corn variety. In some embodiments, the genome of said first corn plant or germplasm is at least 95% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, the first corn plant or germplasm selected from the group consisting of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 and Tuxpeno VEN 692.

In some embodiments of the invention related to the methods disclosed herein, the genome of said second corn plant or germplasm is at least 95% identical to that of an elite variety of corn. In some embodiments, the second corn plant or germplasm is an elite variety of corn. In some embodiments, an elite variety of corn is NP2391.

IV. Transgenic production of corn plants bearing improved traits

In some embodiments, an object of the invention disclosed herein relates to the use of polymorphisms (including, but not limited to SNPs) or traits providing a trait for producing a trailing maize plant by introducing a nucleic acid sequence containing the trait associated with the trait and / or haplotype polymorphism, in the recipient plant.

A donor plant with a nucleic acid sequence that contains an allele and / or haplotype of a sign of optimization of water consumption can be transferred to a recipient plant that does not have this allele and / or haplotype. The nucleic acid sequence can be transferred by crossing a donor plant bearing the trait of optimizing water consumption, with a recipient plant that does not bear this trait (for example, introgression), transforming, transforming or fusing protoplasts, a method for producing doubled haploids, “rescue” the embryo, or any other system nucleic acid transfer. Then, if desired, plant descendants may be selected containing one or more of the alleles and / or haplotypes of the trait for optimizing water consumption disclosed herein. A nucleic acid sequence containing an allele and / or haplotype of a sign of optimizing water consumption can be isolated from a donor plant using methods known in the art, and an isolated nucleic acid sequence can transform a recipient plant by transgenic methods. This can happen with a vector, in a gamete, or in another suitable transfer element, such as a ballistic particle coated with a nucleic acid sequence.

Plant transformation typically involves the construction of an expression vector that will function in plant cells and includes a nucleic acid sequence that contains an allele and / or haplotype associated with a sign of optimizing water consumption, and this vector may contain a gene that provides a sign of optimizing water consumption. This gene is usually under control or functionally linked to one or more regulatory elements, such as a promoter. An expression vector may contain one or more such combinations of a functionally linked gene / regulatory element, provided that at least one of the genes contained in the combinations encodes a sign of optimized water consumption. The vector (s) can be in the form of a plasmid and can be used alone or in combination with other plasmids to provide transgenic plants that have better optimization of water consumption using transformation methods known in the art, such as the Agrobacterium transformation system.

Transformed cells often contain a selectable marker to identify the transformation. A selectable marker is typically suitable for detection by negative selection (by inhibiting the growth of cells that do not contain a selective marker gene) or by positive selection (by screening for a product encoded by a selective marker gene). Many commonly used selectable marker genes for plant transformation are known in the art and include, for example, genes that encode enzymes that metabolically detoxify a selective chemical agent, which may be an antibiotic or herbicide, or genes that encode an altered target that is insensitive to an inhibitor. Several positive selection methods are known in the art, such as mannose selection. Alternatively, to produce plants without the aforementioned marker genes, markerless transformation can be applied, methods of which are also known in the art.

V. Drought tolerant corn plants and germplasm

An object of the invention disclosed herein relates to drought tolerant corn plants and germplasm. As discussed above, the methods of the subject matter disclosed herein can be used to detect, produce and / or select a drought tolerant corn plant or germplasm. In addition to the methods described above, a drought tolerant corn plant or germplasm can be produced by any method by which a marker associated with increased drought tolerance is introduced into the corn or germplasm, including, but not limited to, transformation, transformation or fusion of protoplasts, a method for producing doubled haploids, embryo rescue or any other nucleic acid transfer system.

In some embodiments, the corn plant or germplasm contains an unnatural corn variety. In some embodiments, the corn plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99 % or 100% identical to that of the elite variety of corn. In some embodiments, the genome of said corn plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97% , 99% or 100% identical to that of NP2391.

A corn plant or germplasm may be a descendant of a cross between an elite cultivar of maize and a cultivar of maize that contains an allele associated with increased drought tolerance. In some embodiments, an elite variety of corn is NP2391. In some embodiments, the elite maize variety genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of NP2391. In some embodiments, a variety containing an allele associated with increased drought tolerance is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments of the invention, the genome of a variety containing an allele associated with increased drought tolerance, is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692.

A corn plant or germplasm may be a descendant of introgression, the recurrent parent being an elite variety of corn and the donor contains an allele associated with increased drought tolerance. In some embodiments, the recurrent parent is NP2391. In some embodiments, the recurrent parent genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of NP2391. In some embodiments, the donor is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, the donor gene is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692.

A corn plant or germplasm may be a descendant of a cross between the first elite variety of maize (e.g., a test line) and a descendant of a cross between a second elite variety of corn (e.g., a recurrent parent) and a variety of corn that contains an allele associated with increased drought tolerance (e.g., a donor ) In some embodiments, the first elite variety of maize is NP2460. In some embodiments, the genome of the first elite maize variety is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99 % or 100% identical to that of NP2460. In some embodiments of the invention, the second elite variety of corn is NP2391. In some embodiments, the genome of the second elite variety of maize is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99 % or 100% identical to that of NP2391. In some embodiments, a variety containing an allele associated with increased drought tolerance is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments of the invention, the genome of a variety containing an allele associated with increased drought tolerance, is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692.

A corn plant or germplasm may be a descendant of a cross between the first elite variety of maize and a descendant of introgression, the recurrent parent being the second elite variety of corn and the donor containing an allele associated with increased drought tolerance. In some embodiments, the first elite variety of maize is NP2460. In some embodiments of the invention, the genome of the first elite variety of corn is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99 % or 100% identical to that of NP2460. In some embodiments, the recurrent parent is NP2391. In some embodiments, the recurrent parent genome is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% identical to that of NP2391. In some embodiments, the donor is CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, the donor gene is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692.

Thus, an object of the invention disclosed herein relates, in some embodiments, to Zea mays inbred plants containing one or more alleles associated with a desired sign of optimized water consumption. In some embodiments of the invention:

(I) the sign of optimization of water consumption is grain yield at standard percent moisture (YGSMN), and the favorable allele contains a nucleotide sequence containing A at nucleotide position 270 of the sequence SEQ ID NO: I, G at nucleotide position 216 of the sequence SEQ ID NO: 3; And at nucleotide position 503 of the sequence of SEQ ID NO: 4; CGCG tetranucleotide at nucleotide positions 818-821 of the sequence SEQ ID NO: 5; G at nucleotide position 254 of the sequence SEQ ID NO: 6; dinucleotide GA at nucleotide positions 4497-4498 in the sequence of SEQ ID NO: 7; And at nucleotide position 4641 of the sequence of SEQ ID NO: 7; C or T at nucleotide position 4792 of the sequence SEQ ID NO: 7; T at nucleotide position 4836 of SEQ ID NO: 7; trinucleotide ACT or TCC at nucleotide positions 4979-4981 of the sequence SEQ ID NO: 7; C at nucleotide position 292 of the sequence of SEQ ID NO: 9; And at nucleotide position 166 of the sequence of SEQ ID NO: 10; C at nucleotide position 94 of the sequence of SEQ ID NO: 12; C at nucleotide position 86 of the sequence of SEQ ID NO: 13; G at nucleotide position 89 of the sequence of SEQ ID NO: 13; And at nucleotide position 753 of the sequence SEQ ID NO: 15; G at nucleotide position 755 of the sequence SEQ ID NO: 16; G at nucleotide position 431 of the sequence of SEQ ID NO: 17; And at nucleotide position 309 of the sequence SEQ ID NO: 19; CTGG tetranucleotide at nucleotide positions 773-776 of the sequence SEQ ID NO: 20; a deletion of nucleotide positions 316-324 of the sequence of SEQ ID NO: 21; G at nucleotide position 562 of the sequence of SEQ ID NO: 25; T at nucleotide position 254 of the sequence SEQ ID NO: 27; T at nucleotide position 496 of the sequence SEQ ID NO: 28; G at nucleotide position 398 of the sequence of SEQ ID NO: 30; G at nucleotide position 239 of the sequence SEQ ID NO: 31; G at nucleotide position 208 in the sequence of SEQ ID NO: 32, a dinucleotide CA at a position that corresponds to positions 144-145 of the sequence SEQ ID NO: 34, a nucleotide T at a position that corresponds to position 169 of the sequence SEQ ID NO: 34; nucleotide G at a position that corresponds to position 76 of the sequence SEQ ID NO: 35, nucleotide T at a position that corresponds to position 698 of SEQ ID NO: 36; nucleotide A or G at the position that corresponds to position 386 of the sequence of SEQ ID NO: 37; nucleotide G at a position that corresponds to position 445 of the sequence of SEQ ID NO: 39; nucleotide A at a position that corresponds to position 602 of the sequence of SEQ ID NO: 40; nucleotide G at a position that corresponds to position 190 of the sequence of SEQ ID NO: 41; nucleotide C at the position that corresponds to position 580 of the sequence of SEQ ID NO: 41; trinucleotide TTG at a position that corresponds to positions 266-268 of the sequence SEQ ID NO: 42; nucleotide A at a position that corresponds to position 708 of the sequence SEQ ID NO: 43; nucleotide G at a position which corresponds to position 650 of the sequence of SEQ ID NO: 49; nucleotide A or T at the position that corresponds to position 541 of the sequence of SEQ ID NO: 50; nucleotide T at a position that corresponds to position 428 of the sequence SEQ ID NO: 53; nucleotide C at the position that corresponds to position 491 of the sequence SEQ ID NO: 53; and / or nucleotide A at a position that corresponds to position 126 of the sequence SEQ ID NO: 54; and / or

(II) the sign of optimization of water consumption is the grain moisture at harvest (GMSTP), and the favorable allele contains a nucleotide sequence containing nucleotide A at the position that corresponds to position 254 of the sequence SEQ ID NO: 6; nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 8; nucleotide C at the position that corresponds to position 292 of the sequence SEQ ID NO: 9; nucleotide A at a position that corresponds to position 166 of the sequence of SEQ ID NO: 10; nucleotide G at a position which corresponds to position 148 of the sequence SEQ ID NO: 11; nucleotide A at a position that corresponds to position 35 of the sequence SEQ ID N0: 13; nucleotide G at a position that corresponds to position 432 of the sequence of SEQ ID NO: 14; nucleotide G at a position that corresponds to position 518 of the sequence SEQ ID NO: 18; nucleotide A at a position that corresponds to position 182 of the sequence SEQ ID NO: 19; nucleotide C at the position that corresponds to position 463 of the sequence of SEQ ID NO: 19; CTGG tetranucleotide at a position that corresponds to positions 773-776 of the sequence SEQ ID NO: 20; nucleotide G at a position which corresponds to position 211 of the sequence SEQ ID NO: 22; nucleotide G at a position which corresponds to position 562 of the sequence of SEQ ID NO: 25; nucleotide C at the position that corresponds to position 254 of the sequence of SEQ ID NO: 27; nucleotide G at a position which corresponds to position 239 of the sequence SEQ ID NO: 31; dinucleotide CA at a position which corresponds to position 144-145 of the sequence of SEQ ID NO: 34; nucleotide A at a position that corresponds to position 537 of the sequence of SEQ ID NO: 34; nucleotide A at a position that corresponds to position 386 of the sequence of SEQ ID NO: 37; nucleotide C at the position that corresponds to position 309 of the sequence of SEQ ID NO: 38; nucleotide A at a position that corresponds to position 342 of the sequence of SEQ ID NO: 38; nucleotide C at the position that corresponds to position 445 of the sequence of SEQ ID NO: 39; nucleotide A at a position that corresponds to position 190 of the sequence of SEQ ID NO: 41; nucleotide C at a position which corresponds to position 708 of the sequence SEQ ID NO: 43; nucleotide G at a position which corresponds to position 650 of the sequence of SEQ ID NO: 49; nucleotide C at the position that corresponds to position 428 of the sequence of SEQ ID NO: 53; or nucleotide C at the position that corresponds to position 491 of the sequence of SEQ ID NO: 53; and / or

(III) the sign of optimization of water consumption is the weight of grain per plot (GWTPN), and the favorable allele contains a nucleotide sequence containing T at nucleotide position 518 of the sequence SEQ ID NO: 18.

The object of the invention disclosed herein also relates, in some embodiments, to Zea mays plants containing at least one favorable allele that helps optimize water consumption, and this allele is determined by at least one marker allele containing a polymorphic site and is characterized by a PCR-product amplification obtained in a PCR reaction using an oligonucleotide PCR primer or a plurality of oligonucleotide primers, in particular a pair of oligonucleotide PCR primers P or several pairs of primers, but especially a pair of primers selected from the group consisting of a pair of primers 1 represented by a primer containing the sequence of SEQ ID NO: 118 and a primer containing the sequence of SEQ ID NO: 119; a pair of primers 2 represented by a primer containing the sequence of SEQ ID NO: 120 and a primer containing the sequence of SEQ ID NO: 121; a pair of primers 3 represented by a primer containing the sequence of SEQ ID NO: 122 and a primer containing the sequence of SEQ ID NO: 123; a pair of primers 4 represented by a primer containing the sequence of SEQ ID NO: 124 and a primer containing the sequence of SEQ ID NO: 125; a pair of primers 5 represented by a primer containing the sequence of SEQ ID NO: 126 and a primer containing the sequence of SEQ ID NO: 127; a pair of primers 6 represented by a primer containing the sequence of SEQ ID NO: 128 and a primer containing the sequence of SEQ ID NO: 129; a pair of primers 7 represented by a primer containing the sequence of SEQ ID NO: 130 and a primer containing the sequence of SEQ ID NO: 131; a pair of primers 8 represented by a primer containing the sequence of SEQ ID NO: 132 and a primer containing the sequence of SEQ ID NO: 133; a pair of primers 9 represented by a primer containing the sequence of SEQ ID NO: 134 and a primer containing the sequence of SEQ ID NO: 135; a pair of primers 10 represented by a primer containing the sequence of SEQ ID NO: 136 and a primer containing the sequence of SEQ ID NO: 137; a pair of primers 11 represented by a primer containing the sequence of SEQ ID NO: 138 and a primer containing the sequence of SEQ ID NO: 139; a pair of primers 12 represented by a primer containing the sequence of SEQ ID NO: 140 and a primer containing the sequence of SEQ ID NO: 141; a pair of primers 13 represented by a primer containing the sequence of SEQ ID NO: 142 and a primer containing the sequence of SEQ ID NO: 143; a pair of primers 14 represented by a primer containing the sequence of SEQ ID NO: 144 and a primer containing the sequence of SEQ ID NO: 145; a pair of primers 15 represented by a primer containing the sequence of SEQ ID NO: 146 and a primer containing the sequence of SEQ ID NO: 147; a pair of primers 16 represented by a primer containing the sequence of SEQ ID NO: 148 and a primer containing the sequence of SEQ ID NO: 149; a pair of primers 17 represented by a primer containing the sequence of SEQ ID NO: 150 and a primer containing the sequence of SEQ ID NO: 151; a pair of primers 18 represented by a primer containing the sequence of SEQ ID NO: 152 and a primer containing the sequence of SEQ ID NO: 153; a pair of primers 19 represented by a primer containing the sequence of SEQ ID NO: 154 and a primer containing the sequence of SEQ ID NO: 155; a pair of primers 20 represented by a primer containing the sequence of SEQ ID NO: 156 and a primer containing the sequence of SEQ ID NO: 157; a pair of primers 21 represented by a primer containing the sequence of SEQ ID NO: 158 and a primer containing the sequence of SEQ ID NO: 159, a pair of primers 22 represented by a primer containing the sequence of SEQ ID NO: 160 and a primer containing the sequence of SEQ ID NO: 161; a pair of primers 23 represented by a primer containing the sequence of SEQ ID NO: 162, and a primer containing the sequence of SEQ ID NO: 163; a pair of primers 24 represented by a primer containing the sequence of SEQ ID NO: 164 and a primer containing the sequence of SEQ ID NO: 165; a pair of primers 25 represented by a primer containing the sequence of SEQ ID NO: 166 and a primer containing the sequence of SEQ ID NO: 167; a pair of primers 26, represented by a primer containing the sequence of SEQ ID NO: 168, and a primer containing the sequence of SEQ ID NO: 169; a pair of primers 27 represented by a primer containing the sequence of SEQ ID NO: 170 and a primer containing the sequence of SEQ ID NO: 171; a pair of primers 28 represented by a primer containing the sequence of SEQ ID NO: 172, and a primer containing the sequence of SEQ ID NO: 173, a pair of primers 29 represented by a primer containing the sequence of SEQ ID NO: 174, and a primer containing the sequence of SEQ ID NO: 175; a pair of primers 30 represented by a primer containing the sequence of SEQ ID NO: 176 and a primer containing the sequence of SEQ ID NO: 177; a pair of primers 31 represented by a primer containing the sequence of SEQ ID NO: 178 and a primer containing the sequence of SEQ ID NO: 179; a pair of primers 32 represented by a primer containing the sequence of SEQ ID NO: 180 and a primer containing the sequence of SEQ ID NO: 181; a pair of primers 33, represented by a primer containing the sequence of SEQ ID NO: 182, and a primer containing the sequence of SEQ ID NO: 183; a pair of primers 34 represented by a primer containing the sequence of SEQ ID NO: 184 and a primer containing the sequence of SEQ ID NO: 185; a pair of primers 35 represented by a primer containing the sequence of SEQ ID NO: 186 and a primer containing the sequence of SEQ ID NO: 187; a pair of primers 36 represented by a primer containing the sequence of SEQ ID NO: 188 and a primer containing the sequence of SEQ ID NO: 189; a pair of primers 37, represented by a primer containing the sequence of SEQ ID NO: 190, and a primer containing the sequence of SEQ ID NO: 191; a pair of primers 38 represented by a primer containing the sequence of SEQ ID NO: 192 and a primer containing the sequence of SEQ ID NO: 193; a pair of primers 39, represented by a primer containing the sequence of SEQ ID NO: 194, and a primer containing the sequence of SEQ ID NO: 195; a pair of primers 40 represented by a primer containing the sequence of SEQ ID NO: 196 and a primer containing the sequence of SEQ ID NO: 197; a pair of primers 41 represented by a primer containing the sequence of SEQ ID NO: 198 and a primer containing the sequence of SEQ ID NO: 199; a pair of primers 42 represented by a primer containing the sequence of SEQ ID NO: 200 and a primer containing the sequence of SEQ ID NO: 201; a pair of primers 43 represented by a primer containing the sequence of SEQ ID NO: 202 and a primer containing the sequence of SEQ ID NO: 203; a pair of primers 44 represented by a primer containing the sequence SEQ sequence SEQ ID NO: 204 and a primer containing the sequence SEQ ID NO: 205; a pair of primers 45 represented by a primer containing the sequence SEQ ID NO: 206 and a primer containing the sequence SEQ ID NO: 207; a pair of primers 46 represented by a primer containing the sequence of SEQ ID NO: 208 and a primer containing the sequence of SEQ ID NO: 209; a pair of primers 47 represented by a primer containing the sequence of SEQ ID NO: 210 and a primer containing the sequence of SEQ ID NO: 211; a pair of primers 48 represented by a primer containing the sequence of SEQ ID NO: 212 and a primer containing the sequence of SEQ ID NO: 213; a pair of primers 49 represented by a primer containing the sequence of SEQ ID NO: 214 and a primer containing the sequence of SEQ ID NO: 215; a pair of primers 50 represented by a primer containing the sequence of SEQ ID NO: 216 and a primer containing the sequence of SEQ ID NO: 217; a pair of primers 51 represented by a primer containing the sequence of SEQ ID NO: 218 and a primer containing the sequence of SEQ ID NO: 219; a pair of primers 52 represented by a primer containing the sequence of SEQ ID NO: 220, and a primer containing the sequence of SEQ ID NO: 221, a pair of primers 53 represented by a primer containing the sequence of SEQ ID NO: 222, and a primer containing the sequence of SEQ ID NO: 223; a pair of primers 54 represented by a primer containing the sequence of SEQ ID NO: 224, and a primer containing the sequence of SEQ ID NO: 225, a pair of primers 55 represented by a primer containing the sequence of SEQ ID NO: 226, and a primer containing the sequence of SEQ ID NO: 227; a pair of primers 56 represented by a primer containing the sequence of SEQ ID NO: 228 and a primer containing the sequence of SEQ ID NO: 229; and a pair of primers 57 represented by a primer containing the sequence of SEQ ID NO: 230 and a primer containing the sequence of SEQ ID NO: 231.

In some embodiments, an object of the invention disclosed herein relates to an unnatural corn plant or germplasm having a haplotype in its genome associated with increased drought tolerance. Moreover, in some embodiments of the invention, said haplotype is selected from the group consisting of:

nucleotide G at a position that corresponds to position 100 of the sequence SEQ ID NO: 2, trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at a position that corresponds to position 116 of the sequence SEQ ID NO: 23, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, nucleotide A at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, nucleotide T in position cat paradise corresponds to position 173 sequence SEQ ID NO: 57 and the nucleotide G at a position which corresponds to position 267 sequence SEQ ID NO: 60;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 562 of the sequence SEQ ID NO: 25, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at the position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A in position to which corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position which corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide G at a position that corresponds to position 100, nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 217 of SEQ ID NO: 23, nucleotide C at a position that corresponds to position 746 of the sequence SEQ ID NO: 24, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide G at the position that corresponds to position 472 of the last successive SEQ ID NO: 48, a nucleotide G at a position which corresponds to position 193 sequence SEQ ID NO: 55 and the nucleotide C at a position which corresponds to position 486 sequence SEQ ID NO: 58;

a nucleotide deletion at a position that corresponds to positions 264-271 of SEQ ID NO: 2, a nucleotide A at a position that corresponds to position 4641 of SEQ ID NO: 7, a nucleotide A at a position that corresponds to position 309 of SEQ ID NO: 19, nucleotide A at a position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56, and nucleotide C at the position that corresponds to position 486 of the sequence SEQ ID NO: 58;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 254 of the sequence SEQ ID NO: 27, nucleotide A at the position that corresponds to position 391 of the sequence SEQ ID NO: 33, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, nucleotide G at the position that corresponds to position 193 of the sequence SEQ ID NO: 55, nucleotide C in position cat the original corresponds to position 516 of the sequence SEQ ID NO: 56, nucleotide G at the position that corresponds to position 729 of the sequence SEQ ID NO: 59, and nucleotide G at the position that corresponds to position 267 of the sequence SEQ ID NO: 60;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55, and a nucleotide G at a position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7, nucleotide A at a position that corresponds to position 472 of SEQ ID NO: 48, nucleotide A at a position that corresponds to position 237 of SEQ ID NO: 56, and nucleotide T at a position which corresponds to position 173 of the sequence SEQ ID NO: 57;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 1271 of the sequence SEQ ID NO: 26, nucleotide A at the position that corresponds to position 266 of the sequence SEQ ID NO: 44, nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46, nucleotide A at the position that corresponds to position 472 of the sequence SEQ ID NO: 48, and nucleotide G at the position that corresponds to position 111 of the sequence SEQ ID NO: 51;

nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide C at the position that corresponds to position 258 of the sequence SEQ ID NO: 29, nucleotide G at the position that corresponds to position 87 of the sequence SEQ ID NO: 47, nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48, and a nucleotide G at a position that corresponds to position 193 of the sequence SEQ ID NO: 55;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide A at a position that corresponds to position 309 of the sequence SEQ ID NO: 19, and nucleotide G at the position that corresponds to position 237 of the sequence SEQ ID NO: 56;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19, nucleotide T at the position that corresponds to position 475 of the sequence SEQ ID NO: 45, and nucleotide G at a position which corresponds to position 193 of the sequence SEQ ID NO: 55;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7;

nucleotide A at a position that corresponds to position 4641 of the sequence of SEQ ID NO: 7;

trinucleotide TCC at a position that corresponds to positions 4979-4981 of the sequence SEQ ID NO: 7, and nucleotide C at a position that corresponds to position 386 of the sequence SEQ ID NO: 46;

nucleotide A at a position that corresponds to position 4641 of the sequence SEQ ID NO: 7, and nucleotide G at a position that corresponds to position 472 of the sequence SEQ ID NO: 48,

and their combinations.

In some embodiments, the genome of said corn plant or germplasm is at least 95% identical to that of an elite variety of corn. In some embodiments, an elite variety of corn is NP2391. In some embodiments, a corn plant or germplasm is derived from the cross between an elite variety of corn and an exotic variety of corn. In some embodiments, the genome of said elite variety of maize is at least 95% identical to that of NP2391. In some embodiments, an elite variety of corn is NP2391.

In some embodiments of the invention, the genome of said exotic corn variety is at least 95% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 or Tuxpeno VEN 692. In some embodiments of the invention 32. a corn plant or germplasm according to any 28, wherein the exotic corn variety is selected from the group consisting of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 and Tuxpeno VEN 692. In some embodiments of the invention, said corn plant or germplasm originates from the crossing of the firstlitnogo maize descendant crosses between elite second maize varieties and maize exotic variety.

In some embodiments, the genome of said first elite maize variety is at least 95% identical to that of NP2460. In some embodiments, the first elite variety of maize is NP2460.

In some embodiments, the genome of said second elite variety of maize is at least 95% identical to that of NP2391. In some embodiments of the invention, the second elite variety of corn is NP2391.

In some embodiments of the invention, the genome of said exotic corn variety is at least 95% identical to that of CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, or Tuxpeno VEN 692. In some embodiments, said exotic corn variety is selected from the group consisting of from CML333, CML322, Cateto SP VII, Confite Morocho AYA 38, and Tuxpeno VEN 692.

The subject matter disclosed herein also relates, in some embodiments, to grain and / or kernels produced from a corn plant described herein.

VI. Other compositions

In some embodiments, an object of the invention disclosed herein also relates to primer pairs consisting of a forward primer and a reverse primer, the primers being able to amplify a fragment of a marker allele in a PCR reaction that is genetically linked to or identical to a favorable allele that promotes a phenotype for optimizing water consumption, moreover, said marker allele contains polymorphism, and this polymorphism is diagnostic for a favorable allele. In some embodiments, primer pairs are selected from the group consisting of a pair of primers 1 represented by a primer containing the sequence of SEQ ID NO: 118 and a primer containing the sequence of SEQ ID NO: 119; a pair of primers 2 represented by a primer containing the sequence of SEQ ID NO: 120 and a primer containing the sequence of SEQ ID NO: 121; a pair of primers 3 represented by a primer containing the sequence of SEQ ID NO: 122 and a primer containing the sequence of SEQ ID NO: 123; a pair of primers 4 represented by a primer containing the sequence of SEQ ID NO: 124 and a primer containing the sequence of SEQ ID NO: 125; a pair of primers 5 represented by a primer containing the sequence of SEQ ID NO: 126 and a primer containing the sequence of SEQ ID NO: 127; a pair of primers 6 represented by a primer containing the sequence of SEQ ID NO: 128 and a primer containing the sequence of SEQ ID NO: 129; a pair of primers 7 represented by a primer containing the sequence of SEQ ID NO: 130 and a primer containing the sequence of SEQ ID NO: 131; a pair of primers 8 represented by a primer containing the sequence of SEQ ID NO: 132 and a primer containing the sequence of SEQ ID NO: 133; a pair of primers 9 represented by a primer containing the sequence of SEQ ID NO: 134 and a primer containing the sequence of SEQ ID NO: 135; a pair of primers 10 represented by a primer containing the sequence of SEQ ID NO: 136 and a primer containing the sequence of SEQ ID NO: 137; a pair of primers 11 represented by a primer containing the sequence of SEQ ID NO: 138 and a primer containing the sequence of SEQ ID NO: 139; a pair of primers 12 represented by a primer containing the sequence of SEQ ID NO: 140 and a primer containing the sequence of SEQ ID NO: 141; a pair of primers 13 represented by a primer containing the sequence of SEQ ID NO: 142 and a primer containing the sequence of SEQ ID NO: 143; a pair of primers 14 represented by a primer containing the sequence of SEQ ID NO: 144 and a primer containing the sequence of SEQ ID NO: 145; a pair of primers 15 represented by a primer containing the sequence of SEQ ID NO: 146 and a primer containing the sequence of SEQ ID NO: 147; a pair of primers 16 represented by a primer containing the sequence of SEQ ID NO: 148 and a primer containing the sequence of SEQ ID NO: 149; a pair of primers 17 represented by a primer containing the sequence of SEQ ID NO: 150 and a primer containing the sequence of SEQ ID NO: 151; a pair of primers 18 represented by a primer containing the sequence of SEQ ID NO: 152 and a primer containing the sequence of SEQ ID NO: 153; a pair of primers 19 represented by a primer containing the sequence of SEQ ID NO: 154 and a primer containing the sequence of SEQ ID NO: 155; a pair of primers 20 represented by a primer containing the sequence of SEQ ID NO: 156 and a primer containing the sequence of SEQ ID NO: 157; a pair of primers 21 represented by a primer containing the sequence of SEQ ID NO: 158 and a primer containing the sequence of SEQ ID NO: 159, a pair of primers 22 represented by a primer containing the sequence of SEQ ID NO: 160 and a primer containing the sequence of SEQ ID NO: 161; a pair of primers 23 represented by a primer containing the sequence of SEQ ID NO: 162, and a primer containing the sequence of SEQ ID NO: 163; a pair of primers 24 represented by a primer containing the sequence of SEQ ID NO: 164 and a primer containing the sequence of SEQ ID NO: 165; a pair of primers 25 represented by a primer containing the sequence of SEQ ID NO: 166 and a primer containing the sequence of SEQ ID NO: 167; a pair of primers 26, represented by a primer containing the sequence of SEQ ID NO: 168, and a primer containing the sequence of SEQ ID NO: 169; a pair of primers 27 represented by a primer containing the sequence of SEQ ID NO: 170 and a primer containing the sequence of SEQ ID NO: 171; a pair of primers 28 represented by a primer containing the sequence of SEQ ID NO: 172, and a primer containing the sequence of SEQ ID NO: 173, a pair of primers 29 represented by a primer containing the sequence of SEQ ID NO: 174, and a primer containing the sequence of SEQ ID NO: 175; a pair of primers 30 represented by a primer containing the sequence of SEQ ID NO: 176 and a primer containing the sequence of SEQ ID NO: 177; a pair of primers 31 represented by a primer containing the sequence of SEQ ID NO: 178 and a primer containing the sequence of SEQ ID NO: 179; a pair of primers 32 represented by a primer containing the sequence of SEQ ID NO: 180 and a primer containing the sequence of SEQ ID NO: 181; a pair of primers 33, represented by a primer containing the sequence of SEQ ID NO: 182, and a primer containing the sequence of SEQ ID NO: 183; a pair of primers 34 represented by a primer containing the sequence of SEQ ID NO: 184 and a primer containing the sequence of SEQ ID NO: 185; a pair of primers 35 represented by a primer containing the sequence of SEQ ID NO: 186 and a primer containing the sequence of SEQ ID NO: 187; a pair of primers 36 represented by a primer containing the sequence of SEQ ID NO: 188 and a primer containing the sequence of SEQ ID NO: 189; a pair of primers 37, represented by a primer containing the sequence of SEQ ID NO: 190, and a primer containing the sequence of SEQ ID NO: 191; a pair of primers 38 represented by a primer containing the sequence of SEQ ID NO: 192 and a primer containing the sequence of SEQ ID NO: 193; a pair of primers 39, represented by a primer containing the sequence of SEQ ID NO: 194, and a primer containing the sequence of SEQ ID NO: 195; a pair of primers 40 represented by a primer containing the sequence of SEQ ID NO: 196 and a primer containing the sequence of SEQ ID NO: 197; a pair of primers 41 represented by a primer containing the sequence of SEQ ID NO: 198 and a primer containing the sequence of SEQ ID NO: 199; a pair of primers 42 represented by a primer containing the sequence of SEQ ID NO: 200 and a primer containing the sequence of SEQ ID NO: 201; a pair of primers 43 represented by a primer containing the sequence of SEQ ID NO: 202 and a primer containing the sequence of SEQ ID NO: 203; a pair of primers 44 represented by a primer containing the sequence SEQ sequence SEQ ID NO: 204 and a primer containing the sequence SEQ ID NO: 205; a pair of primers 45 represented by a primer containing the sequence SEQ ID NO: 206 and a primer containing the sequence SEQ ID NO: 207; a pair of primers 46 represented by a primer containing the sequence of SEQ ID NO: 208 and a primer containing the sequence of SEQ ID NO: 209; a pair of primers 47 represented by a primer containing the sequence of SEQ ID NO: 210 and a primer containing the sequence of SEQ ID NO: 211; a pair of primers 48 represented by a primer containing the sequence of SEQ ID NO: 212 and a primer containing the sequence of SEQ ID NO: 213; a pair of primers 49 represented by a primer containing the sequence of SEQ ID NO: 214 and a primer containing the sequence of SEQ ID NO: 215; a pair of primers 50 represented by a primer containing the sequence of SEQ ID NO: 216 and a primer containing the sequence of SEQ ID NO: 217; a pair of primers 51 represented by a primer containing the sequence of SEQ ID NO: 218 and a primer containing the sequence of SEQ ID NO: 219; a pair of primers 52 represented by a primer containing the sequence of SEQ ID NO: 220, and a primer containing the sequence of SEQ ID NO: 221, a pair of primers 53 represented by a primer containing the sequence of SEQ ID NO: 222, and a primer containing the sequence of SEQ ID NO: 223; a pair of primers 54 represented by a primer containing the sequence of SEQ ID NO: 224, and a primer containing the sequence of SEQ ID NO: 225, a pair of primers 55 represented by a primer containing the sequence of SEQ ID NO: 226, and a primer containing the sequence of SEQ ID NO: 227; a pair of primers 56 represented by a primer containing the sequence of SEQ ID NO: 228 and a primer containing the sequence of SEQ ID NO: 229; and a pair of primers 57 represented by a primer containing the sequence of SEQ ID NO: 230 and a primer containing the sequence of SEQ ID NO: 231.

EXAMPLES

The following examples relate to illustrative embodiments of the invention. In light of the present disclosure and the general level of the art, it will be understood by those skilled in the art that the following examples are intended to be used only as samples and that numerous changes, modifications, and changes can be applied without departing from the scope of the subject matter disclosed herein.

INTRODUCTION TO EXAMPLES

To assess the allele values during drought, different germplasm was screened in controlled field experiments containing a control treatment with full irrigation and a treatment with limited irrigation. The purpose of full irrigation treatment was to ensure that water did not limit crop productivity. On the contrary, the purpose of limited irrigation processing was to ensure that water became the main limiting limiter on grain yield. The main effects (e.g., treatment and genotype) and interactions (e.g., genotype x treatment) can be determined when two treatments are applied in the field next to each other. Moreover, for each genotype in the panel, phenotypes associated with drought can be quantified, thereby allowing marker: trait associations.

In practice, the limited irrigation treatment method can vary widely depending on the germplasm being screened, such as soil, local climatic conditions, pre-season water supply, and season water supply, and these are just some of the factors. Initially, a place is identified where seasonal rainfall is small (to minimize the chance of inadvertent hydration), and which is suitable for growing crops. In addition, it may be important to determine the timing of exposure to stress, so that a goal is defined in order to ensure that the screening sequence at a given site is consistent from year to year or from location to location. The intensity of the treatment or, in some cases, the loss of crop desired in the case of processing with limited irrigation can also be taken into account. When choosing a treatment intensity that is too light, genotypic variation may not be detected. Choosing a processing intensity that is too heavy can lead to too many errors. Once the timing of the stress exposure is determined and the processing intensity is described, irrigation can be carried out in such a way as to meet these goals.

General methods for assessing and evaluating drought tolerance can be found in Salekdeh et al., 2009 and US Pat. Nos. 6,635,803, 7,314,757, 7,332,651 and 7,432,416.

Example 1

Evaluation of phenotypic data

In order to identify the alleles that were associated with the optimization of water consumption, hybrids were grown at different stages in different locations and evaluated the optimization of water consumption. In this analysis, four traits were tested at stages 2-3: YGSMN (grain yield at a standard percentage of moisture%), GMSTP (grain moisture at harvest time), GWTPN (grain weight per plot) and PYREC (recovery percent yield). The distribution of phenotypic data of line hybrids by location and testers was determined for YGSMN, GMSTP, GWTPN and PYREC. Average values for YGSMN, GMSTP and GWTPN were 165.41 bushels / acre, 18.94% and 20.0 bushels / acre, respectively. Phenotypic data from selected studies included information from four locations. The number of observations at these locations ranged from 311 to 1456. A total of 575 inbreds were estimated in crosses with up to 47 different inbred testers. The number of observations of inbred lines crossed with a specific tester ranged from 242 to 575 at all locations.

When testing the associations between potential markers and these three attributes, two analytical approaches were used: mixed linear models - (TASSEL) and Quantitative Inbred Pedigree Disequilibrium Test (hereinafter referred to as "QIPDT2").

Example 2

Phenotypic adjustments

The use of the data obtained in stage 2-3 for mapping associations is not a traditional approach, and there are several aspects of its analysis that need to be considered. Moreover, for phenotyping, hybrids with different testers were used, and not lines as such, while both statistical methods (TASSEL and QIPDT2) were developed for data on inbred lines that require a single trait value for each line. In order to obtain a unique trait value for each inbred line that can be compared with its genotype, phenotypic corrections were necessary to help control the effect of the tester and / or location. Additional factors (e.g., group maturity) were not considered to avoid additional reductions in the degrees of freedom or the size of the subsets of the samples.

To perform phenotypic corrections, analyzes of mixed linear models were performed in two different statistical packages SAS / JMP and R, which were designed so that approaches with a mixed model for a large data set were used correctly. Since the approaches yielded very close results, SAS / JMP results were applied to subsequent stages of data analysis.

When analyzing the “full model”, the effects of both location and testers were included in the location model as follows:

Phenotype = location effect (random) + line effect (random) + tester effect (fixed) + error

The location model was applied for each of the 4 selected locations as follows:

Phenotype = line effect (random) + tester effect (fixed) + error The “tester” model was applied for each of the 4 selected subsets of lines crossed with a specific tester, as follows:

Phenotype = location effect (random) + line effect (random) + error

Models were evaluated for convergence, covariance estimation, significance of fixed effects, etc. The best linear unbiased predictors (BLUP) for line effects were used as corrected genotypes. In some cases, the proposed mixed models did not converge or there was a problem with the estimation of the line effects due to the lack of replication. In each such case, the line effect was removed from the model and residual values were used as a rough way of capturing the line effects (additional replication was obtained later in the analysis of associations, when each biallelic locus was represented by the total number of inbred lines of each group).

A solution for random line effects (BLUP) was obtained from mixed models that converged.

Example 3

Genotypic data

A total of 2,189 lines for which phenotypic data were collected in any of the selected studies were also genotyped. A total of 95 polymorphisms corresponding to about 57 candidate genes were evaluated in inbred lines. After removal of monomorphic cases and SNPs with allele frequencies of less than about 0.01, 85 candidate polymorphisms were tested for association in TASSEL. In addition, 153 random polymorphisms were genotyped in inbred lines. After filtering, 149 random polymorphisms were also analyzed for association in TASSEL as anonymous candidates.

Example 4

Association Analysis Methodologies

Association-based mapping (often called non-equilibrium linkage mapping) has become a powerful tool for uncovering genetic control of complex traits. Mapping based on association analysis relies on a large number of generations and, therefore, recombination capabilities in the history of the species that allow the removal of an association between QTL and any marker not closely linked to it (Jannink & Walsh, 2001). One of the most important steps in mapping analysis based on association analysis is to control population structure. The population structure can lead to false correlations between markers and phenotypes, increasing the possibility of a false positive result.

Kinship analysis. The method implemented in TASSEL uses a kinship matrix in the mixed model approach to control genetic correlations between the lines. Kinship analysis was performed using genotypic data from 153 randomly selected SNP tests. A method for evaluating kinship relationships was adopted, based on Zhao et al., 2007. Scripts were created to calculate kinship ratios, which were defined simply as the proportion of total alleles for each pair of individuals (K pShared). Zhao et al used the proportion of total haplotypes as coefficients of their affinity. The matrix of coefficients K was included in TASSEL for some association models to evaluate the control of false associations due to the close interconnectedness of the lines in the panel. Kindness matrix calculator. Matrix K was calculated for a set of inbred lines. The kij affinity coefficient was calculated as the fraction of total alleles for all loci between the two lines i and j, and kij = kji, kii = 1.

Analysis of the structure of the population. Analysis with Structure software (Pritchard et al., 2000) was performed using genotypic data from 153 randomly selected SNP tests. A linkage model was used that included an admixture of population and linkage between markers. The probabilities of population structures with k ranging from 1 to 15 subpopulations were determined using a preliminary period of 50,000 followed by 50,000 repetitions of MSMS. Four replications were performed for each k value. The estimated logarithm of the data probability Pr (X | K) for each value of k was plotted to select the appropriate number of subpopulations to be included in the covariance matrix.

The probability for the determinant k increased along with the number of checked 1 s. A value of k equal to 10 was used as the number of subpopulations for analysis of associations. A table with the derived pedigree, containing the share of each subpopulation contributing to the pedigree of each inbred, was used as a series of covariants in the association testing model.

Analysis of the main components. Principal Component Analysis (PCA) or Eigenvalue Analysis was used as an alternative to the Structure software to derive the population structure from genotypic data. PCA has some advantages over Structure, such as the ability to process large data sets for significantly shorter periods of time and the lack of the need to select a specific number of subpopulations. PCA was performed using SMARTPCA software, which is part of Eigenstrat (Price et al., 2006). Ten eigenvectors and their corresponding eigenvalues for each of the lines were used as another covariant series for models of the TASSEL association.

Example 5

TASSEL analysis

Association models in TASSEL. Table 6 shows the various models used in TASSEL. For the YGSMN and GMSTP phenotypes, adjusted by location and testers, six (6) models were run and compared. Only Model 4 was launched for all subsets of locations and testers.

Table 6 Association Models Used by TASSEL General linear models Mixed linear models 1) Correction. Phenotype = Marker 4) Correction. Phenotype = Marker + K (pshared) * 2) Correction. Phenotype = Marker + Q (Structure) 5) Correction. Phenotype = Marker + K (pshared) + Q (Structure) 3) Correction. Phenotype = Marker + PCA (eigenvalues) 6) Correction. Phenotype = Marker + K (pshared) + PCA (eigenvalues)

The TASSEL GLM procedure used the ability to perform permutations to find out the level of experimental errors adjusted for the accumulation of false-positive results when performing multiple comparisons. A total of 10,000 permutations were applied for data on water consumption optimization. The MLM procedure did not include an amendment for repeated testing. The Bonferroni correction was applied a posteriori to avoid the accumulation of false-positive results.

Example 6

Association Analysis Using QIPDT2

QIPDT2 (Quantitative Inbred Pedigree Disequilibrium Test 2) was used to map associations, which has the advantage of using inbred pedigree information, which can give higher statistical certainty and fewer false-positive results with better control over the population structure (Stich et al. 2006, TAG 113: 1121 -1130). QIPDT2 is an improvement on QIPDT, originally designed for mapping human disease genes (Zhang et al., 2001. Genetic Epidemiol 21: 370-375 - See link from Stich et al. 2006). The advantage of QIPDT2 is that this method can be easily applied to materials from the early stages of dilution (for example, stage 2 and 3), because phenotypic data on such materials were collected for breeding purposes. Generally speaking, materials from the early stages of dilution are similar to the lines in the well-known populations of grouped associations (NAMs) that have been developed to use both linkage and non-equilibrium linkage for QTL mapping. The original QIPDT is a statistical criterion for T, which is calculated as follows (Stich et al. 2006):

, следуя из N(0, 1) при H₀, $$T=\frac{{\displaystyle {\sum }_{k=\mathrm{one}}^p{D}_k}}{\sqrt{{\displaystyle {\sum }_{k=\mathrm{one}}^{\mathrm{<figure-callout\; id="2"\; label="p\; D\; k"\; filenames="00000013.png,00000015.png"\; state="\{\{state\}\}">p\; </figure-callout>}}{D}_k^{}{}_2^{}}}}$$

, following from N (0, 1) for H ₀ ,

, $$E\left({\displaystyle \sum _{k=1}^p{D}_k}\right)=0$$

при H₀, $$D_k={\displaystyle \sum _{i=\mathrm{one}}^{n_k}{U}_{jk}}$$

, $$E\left({\displaystyle \sum _{k=\mathrm{one}}^p{D}_k}\right)=0$$

at H ₀ ,

, $$U_{jk}={\displaystyle \sum _{i=\mathrm{one}}^{t_{jk}}\left(Y_{ijk}-\overline{Y_k}\right)}{X}_{ijk}$$

,

- среднее значение признака для улучшенной родословной k, $$\overline{Y_k}$$

- the average value of the trait for the improved pedigree k,

x _ijk - marker value (-1, 0, 1).

In a general approach, the T value is calculated for each SNP, and its p value is found from the standard normal distribution. Although this approach is applicable to verify the statistical significance of the association, it does not provide an estimate of the magnitude of the genetic effect of SNP, nor the relative genetic contribution to the total phenotypic variance.

Thus, the overall QIPDT approach has been improved with a regression model called here “QIPDT2"; the original method is then called QIPDT 1.

The QIPDT2 model can be written as:

y _ki = β ₀ + β ₁ x _ki + e _ki ,

where y _ki is the adjusted phenotypic value for an individual i in the pedigree k; x _ki represents the genotypic value of the encoded marker; β ₀ is an intercept; β ₁ is the regression coefficient or genetic effect of SNP in question. Note that the methods for adjusting phenotypic values and genotypes of encoded markers are the same as those used by Stich et al. 2006. Using this model, for each SNP, both the genetic effect and R ² can be estimated. It is important to note that phenotypic data were pre-adjusted to exclude effects from testers and / or locations, before they were further adjusted for the pedigree structure, this adjustment was necessary to implement a complex model in QIPDT2. The pre-adjustment methods were the same as previously described for the TASSEL analysis. Association Models in QIPDT2. Association data was obtained for the entire dataset and individual subsets for location locations and testers using both the QIPDT1 and QIPDT2 approaches. As in the analysis with TASSEL, phenotypic data were adjusted for locations and / or testers, depending on which subset was used. As a result, one adjusted phenotypic value was obtained (either BLUP line values or residual model values) for each inbred, which contains a combination of all genetic effects for the inbred and only a random residual value.

Prior to QIPDT analysis, all inbreeds were grouped into different nuclear families according to their parental lines. The use of the nuclear family was supposed to give a more controlled population structure than the improved pedigrees used by Stich et al. 2006. For QIPDT 1, test statistics (Z value) and corresponding p value were estimated for each SNP; for QIPDT2, test statistics (Z value) and the corresponding p value were obtained from a simple regression model, along with R ² , for each SNP. QIPDT2 was more reliable than QIPDT 1 in terms of p values. Since QIPDT2 also provided estimates (R ² ) for the relative contribution of each SNP, QIPDT2 was used to report on association data obtained using the QIPDT approach.

Example 7

The value and contribution of favorable alleles

in phenotypes of water consumption optimization

The p values and the observed contributions of each favorable allele to the phenotypes of water consumption optimization YGSMN, GMSTP and GWTPN were calculated. These values are shown in tables 7-9. In Tables 7–9, the term “contribution” refers to the contribution that was calculated to have a favorable allele on the observed phenotype, taking into account average values of 201.68 bushels / acre, 18.95% and 25.29 bushels / plot for YGSMN, GMSTP and GWTPN, respectively. In Tables 7-9, the “contribution” is expressed in bushels / acre, percent and bushels / section for YGSMN, GMSTP and GWTPN, respectively.

Table 7 Contributions of favorable alleles to increased optimization of water consumption identified by TASSEL and OIPDT2 SEQ ID NO: SNP Position F U Sign Contribution P value 12 292 FROM BUT Gmstp 0.973536 0.000509 37 145 FROM BUT Gmstp 0.2769 0.000315 39 169 T BUT Gmstp 0.2721405 0.00034675 42 386 BUT G Gmstp 0.379311 0.000192 51 708 FROM BUT Gmstp 0.31989 0.000287 55 491 FROM G Gmstp 0.544187 0.0001335 56 428 G BUT Gmstp 0.347253 0.000573

Table 8 Contribution of favorable alleles to increased water consumption optimization identified by TASSEL SEQ ID NO: SNP Position F U Sign P value Contribution one 428 BUT G YGSMN 0.0084 11.3070462 2 216 G T YGSMN 0.000054594 4.15 3 506 BUT G YGSMN 0.0005806 2.187 four 818-821 - Cgcg YGSMN 0.0035 14.5878562 5 254 G A YGSMN 0.00022694 1.6857 A G Gmstp 5.62 × 10 ^-7 0.3725 6 186-188 G A YGSMN 0.007 6.8929277 7 526 A FROM YGSMN 0.000211972 3.3256 7 * 526 A FROM YGSMN 0.0026 7.3903226 8 615-616 - GA YGSMN 0.03 5.665 9 375 A G YGSMN 0.0143 6.5897654 10 331 A G YGSMN 0.000435023 3.01738 10* 331 A G YGSMN 0.0026 7.3903226 eleven 210 A G Gmstp 0.2431269 0.599 12 292 FROM A YGSMN 0.0031 4.2222 13 166 A G YGSMN 0.0263 5.4031514 A G Gmstp 0.000204245 1.1278 fifteen 94 FROM G YGSMN 4.38 × 10 ^-6 1.3181 fifteen* 94 FROM G YGSMN 0.0309 7.624524 16 35 A T Gmstp 0.00095646 0.086 17 146 FROM A YGSMN 0.0071 8.327576 eighteen 149 G FROM YGSMN 0.000650794 1.312 19 432 G A Gmstp 5.47 × 10 ^-15 0.0393 twenty 753 A G YGSMN 0.0025 2.1981 21 755 G A YGSMN 0.000486298 2.2198 22 431 G FROM Gmstp 5.43 × 10 ^-6 0.4939 23 518 G T Gmstp 7.35 × 10 ^-5 1.2629 24 387 FROM G Gmstp 0.00039766 0.4522 25 660 BUT G Gmstp 0.00039306 0.4219 26 536 T FROM YGSMN 0.000740946 0.7923 27 773-776 FROM G YGSMN 0.000138841 0.9736 FROM G Gmstp 0.000124719 0.7974 28 310 T BUT YGSMN 1.87 × 10 ^-7 1.433 29th 211 G BUT Gmstp 0.00034028 0.5831 thirty 401 G BUT YGSMN 0.0102 6.4804254 G BUT Gmstp 0.000177776 0.6844 31 254 BUT G YGSMN 0.0044 8.7386037 G BUT Gmstp 0.00125 1.8112 32 439 BUT G YGSMN 0.025 5.136 33 384 G BUT YGSMN 0.015 6.284 35 239 G BUT YGSMN 0.0495 4.6259439 G BUT Gmstp 0.000154145 1.4141 36 208 G BUT YGSMN 0.000249875 1.7148 37 145 FROM BUT YGSMN 0.00029249 3.16538 38 535 BUT T Gmstp 0.000180209 0.1236 39 169 T BUT Gmstp 0.000124333 1.2461 40 76 G BUT YGSMN 0.0012 11.9039947 41 724 BUT G YGSMN 2.71 × 10 ^-5 4.65472 42 386 BUT G YGSMN 0.0037 11.255257 43 375 BUT G Gmstp 0.000221511 0.6653 44 309 FROM G Gmstp 0.0011 0.1152 45 342 BUT FROM Gmstp 0.266801841 0.8445 46 445 G FROM YGSMN 0.000032821 1.6764 47 602 BUT T YGSMN 0.000769319 3.7163 48 190 G BUT YGSMN 0.000297308 3.369 48 * 190 G BUT YGSMN 0.0054 8.0700349 49 593 FROM G YGSMN 0.001142836 10.5852 49 * 593 FROM G YGSMN 0.0282 7.642183 fifty 266-267 - AA YGSMN 0.017 6.724 51 708 BUT FROM YGSMN 0.0054 7.3294598 FROM BUT Gmstp 2.42 × 10 ^-5 0.3221 52 648 G BUT YGSMN 0.0026 10.9837972 53 541 A T YGSMN 0.0003 10.3325637 54 442 FROM G YGSMN 0.000013938 11.0737 55 491 FROM G YGSMN 0.000238135 7.1354 55 * 491 FROM G YGSMN 0.0446 9.1504902 56 428 BUT G YGSMN 0.000578625 0.7024 57 126 BUT G YGSMN 6.83 × 10 ^-5 3.70653 BUT G Gmstp 6.19 × 10 ^-5 0.5342 * Data refer to hybrid testing

Table 9 Contributions of Favorable Alleles to Improved Water Consumption Optimization Identified by OIPDT2 SEQ ID NO: SNP Position F U Sign Contribution P value 12 292 FROM BUT Gmstp 0.973536 0.000509 fourteen 148 G T Gmstp 0.739413 0.000003 23 518 T G Gwtpn 3.438703 0.000198 37 145 FROM BUT Gmstp 0.2769 0.000315 39 169 t BUT Gmstp 0.2721405 0.00034675 42 386 BUT G Gmstp 0.379311 0.000192 46 445 FROM G Gmstp 0.777738 0.000547 48 190 BUT G Gmstp 1.47593 0.000274 51 708 FROM BUT Gmstp 0.31989 0.000287 52 648 G BUT Gmstp 0.450848 0.000111 55 491 FROM G Gmstp 0.544187 0.0001335 56 428 G BUT Gmstp 0.347253 0.000573

Materials and methods used in examples 8-12

NP2391 is an elite variety of corn with non-rigid stems. NP2391 is described in US patent No. 7166783. NP2391 contains the G allele at position 87 of SEQ ID NO: 47, the G allele at position 386 of SEQ ID NO: 46, the G allele at positions 4979-4981 of SEQ ID NO: 7, the C allele at position 4641 of SEQ ID sequence NO: 7, allele A at position 472 of SEQ ID NO: 48, allele G at position 237 of SEQ ID NO: 56, allele A at position 516 of SEQ ID NO: 56, allele A at position 266 of SEQ ID NO: 44, the T allele at position 475 of the sequence SEQ ID NO: 45, the T allele at position 173 of the sequence SEQ ID NO: 57, allele C at position 746 of SEQ ID NO: 24, allele A at position 391 of SEQ ID NO: 33, allele C at position 258 of SEQ ID NO: 29, allele A at position 217 of SEQ ID NO: 23, allele G at position 116 of SEQ ID NO: 23, allele G at position 463 of SEQ ID NO: 19, allele T at position 309 of SEQ ID NO: 19, allele D at positions 264-271 of SEQ ID NO: 2, allele G at position 100 of the sequence SEQ ID NO: 2, allele C at position 486 of the sequence SEQ ID NO: 58, allele G at position 111 of the sequence SEQ ID NO: 51, allele G at position 254 of SEQ ID NO: 27, allele G at position 729 of SEQ ID NO: 59, allele G at position 267 of SEQ ID NO: 60, allele G at position 562 of SEQ ID NO: 25, C allele position 1271 of the sequence SEQ ID NO: 26 and the allele G at position 193 of the sequence SEQ ID NO: 55. See figure 1.

NP2460 is an elite variety of corn with hard stalks. NP2460 is described in US patent No. 7122726. NP2460 contains allele C at position 386 of SEQ ID NO: 46, allele A at positions 4979-4981 of SEQ ID NO: 7, allele A at position 4641 of SEQ ID NO: 7, allele G at position 472 of SEQ ID NO : 48, allele G at position 237 of SEQ ID NO: 56, allele C at position 516 of SEQ ID NO: 56, allele C at position 266 of SEQ ID NO: 44, allele C at position 475 of SEQ ID NO: 45 , allele G at position 173 of the sequence SEQ ID NO: 57, allele C at position 746 of the sequence SEQ ID NO: 24, allele A at position 3 91 sequences of SEQ ID NO: 33, allele T at position 258 of SEQ ID NO: 29, allele A at position 217 of SEQ ID NO: 23, allele G at position 116 of SEQ ID NO: 23, allele C at position 463 of the sequence SEQ ID NO: 19, allele C at position 309 of the sequence SEQ ID NO: 19, allele D at positions 264-271 of the sequence SEQ ID NO: 2, allele G at position 100 of the sequence SEQ ID NO: 2, allele C at position 486 of the sequence SEQ ID NO: 58, allele G at position 254 of SEQ ID NO: 27, allele G at position 729 of SEQ ID NO: 59, allele G at position 267 after ovatelnosti SEQ ID NO: 60, allele G at position 562 sequence SEQ ID NO: 25, C allele at position 1271 sequence SEQ ID NO: 26 and the A allele at position 193 sequence SEQ ID NO:. 55. See figure 1.

CML333 is an exotic inbred corn variety from the International Corn and Wheat Improvement Center (CIMMYT) in Mexico. CML333 is known to be resistant to both the southwestern corn drill and grass scoop. CML333 contains allele A at positions 4979-4981 of the sequence of SEQ ID NO: 7, allele G at position 472 of SEQ ID NO: 48, allele G at position 237 of SEQ ID NO: 56, allele G at position 173 of SEQ ID NO : 57, allele G at 0172A, allele A at position 116 of SEQ ID NO: 23, allele A at position 100 of SEQ ID NO: 2 and allele A at position 267 of SEQ ID NO: 60. See FIG. 1.

CML322 is an exotic inbred corn variety from the International Corn and Wheat Improvement Center (CIMMYT) in Mexico. CML322 contains allele C at position 386 of SEQ ID NO: 46, allele A at positions 4979-4981 of SEQ ID NO: 7, allele G at position 472 of SEQ ID NO: 48, allele C at position 266 of SEQ ID NO: 44, allele C at position 309 of SEQ ID NO: 19, allele C at position 111 of SEQ ID NO: 51, allele A at position 562 of SEQ ID NO: 25 and allele A at position 1271 of SEQ ID NO: 26. See figure 1.

Cateto SP VII is an exotic corn variety native to Brazil. Although this variety shows a high ability to combine with many varieties of corn, it has a relatively low yield. Cateto SP VII contains allele A at position 87 of SEQ ID NO: 47, allele A at position 4641 of SEQ ID NO: 7, allele G at position 472 of SEQ ID NO: 48, allele C at position 266 of SEQ ID NO: 44, allele A at position 746 of SEQ ID NO: 24, allele T at position 258 of SEQ ID NO: 29, allele G at position 217 of SEQ ID NO: 23, allele A at position 100 of SEQ ID NO: 2, allele A at position 486 of the sequence SEQ ID NO: 58 and allele A at position 193 of the sequence SEQ ID NO: 55. See figure 1.

Confite Morocho AYA 38 is an exotic corn variety native to Peru. Despite the fact that it is resistant to helminthosporious leaf spot, it is susceptible to rust damage. Confite Morocho AYA 38 contains allele A at position 4641 of SEQ ID NO: 7, allele C at position 237 of SEQ ID NO: 56, allele G at position 391 of SEQ ID NO: 33, allele C at position 309 of SEQ ID NO : 19, the insertion at positions 264-271 of the sequence SEQ ID NO: 2 and the allele A at position 486 of the sequence SEQ ID NO: 58. See figure 1.

Tuxpeno VEN 692 is an exotic corn variety native to Venezuela. It is highly resistant to both helminthosporious leaf spot and rust. Tuxpeno VEN 692 contains allele A at position 4641 of SEQ ID NO: 7, allele C at position 237 of SEQ ID NO: 56, allele G at position 258 of SEQ ID NO: 29, allele C at position 463 of SEQ ID NO: 19 and allele A at position 193 of the sequence SEQ ID NO: 55. See figure 1.

Corn plants of variety NP23 91 were crossed with 134 exotic corn varieties, including CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 and Tuxpeno VEN 692. The offspring of these crosses was crossed back and forth with NP23 91 for five generations to create NP23 91-exotic hybrids. Segment introgressions from the shaggy kinase gene (GenBank® AY103545 database access number, incorporated herein by reference) were found in NP23 91 exotic hybrids representing 42 exotic donors (CML333, CML322, Cateto SP VII, Confite Morocho AYA 38 Tuxpeno VEN 692, CML69, HH5982, TLT0766, CML103, M37W, TLZ0845, AGG742, NC358, P39, Serrano GUA 3, Mochero LBQ 17 KXI0970, 6B209, Cholito BOV 705 CML228, Coroico Amarillo, 8B006, EE8001, Enano Granova MD SAN, XPRR001, B97, Cacao SAS 327, Tx303, Clavito ECU 366, Early Caribbean MAR 10, Patillo BOV 502, Rabo De Zorro AHK 325 Shajatu AHK 120, Shoe Peg PI269743, St. Croix IVC 2, Oh7B, Polio VEN 336, Tzi8 and Oh43). Each of the NP23 91-exotic hybrids containing segmental introgression in the shaggy kinase gene self-pollinated for two generations, selecting offspring containing the exotic donor genotype at positions 4979-4981 of the sequence SEQ ID NO: 7 / position 4641 of the sequence SEQ ID NO: 7. Two lines were selected from the progeny of each self-pollination of an NP2391-exotic hybrid: one homozygous exotic donor genotype at positions 4979-4981 of SEQ ID NO: 7 / position 4641 of SEQ ID NO: 7 and another homozygous exotic donor enotip NP2391 positions 4979-4981 in the sequence SEQ ID NO: 7/4641 sequence position SEQ ID NO: 7. Each of these lines were crossed with NP2460, to create the F1 hybrid line. In addition, the NP2460 was crossed directly with the NP2391 to create an F1 control hybrid.

F1 hybrids were evaluated in four arid locations (La Salle, Colorado, USA, Gilroy, California, USA; Los Andes, Chile and Granaros, Chile), with six repetitions of processing at each location by constructing limited randomized blocks, as well as in twelve areas with optimal conditions with one repetition. Treatments with the stressful effects of drought were carried out during pollination, and they consisted of a period of water shortage that could reduce grain yield by about 40-60%. The timing of each treatment with the stressful effects of drought was determined by the type of soil and local climate (based on which the water holding capacity and evaporation rate (ET) were estimated or measured). Normal irrigation was stopped 3-4 weeks before the middle of the dusting period so that the soil moisture level dropped to a critical level, which was reached about 7 days before dusting. As soon as the soil dried up to a critical level, an irrigation deficit regime was established (about 40% ET). Drought stress treatments continued for two weeks after the middle of the dusting period, after which normal irrigation was resumed.

Drought tolerance was assessed by measuring grain yield at standard percent moisture (YGSMN) and grain moisture at harvest time (GMSTP). Qualitative control of statistical data was carried out by constructing a data distribution. Residues were obtained using the following model:

Y = µ + location + replication (location) + family + allele (family),

where Y is a dependent phenotype and µ is a phenotypic mean; location and replication (location) were random. Family and allele (family) were fixed. Residues were analyzed by replication within the family and labeled in accordance with specified criteria, depending on the trait being evaluated. The final analysis was carried out both for individual locations and for locations combined using the following model:

Y = µ + replication + family + allele (family) + replication * family,

where Y is a dependent phenotype and μ is a phenotypic mean. Replications were random. Family and allele (family) were fixed. The least squares method was calculated and Student's T-test was used for pairwise comparisons.

As shown in table 10, six F1 hybrids obtained by crossing NP2460 with a line homozygous for the exotic donor genotype at positions 4979-4981 of SEQ ID NO: 7 / position 4641 of SEQ ID NO: 7 showed increased drought tolerance.

Table 10 Comparison of Hybrid NP2460 with respect to SEO ID NO: 7 Hybrid F1 Productivity (Bushel / Acre) Difference in drought conditions (bushel / acre) Optimal conditions for growing corn Drought vs. hybrid control vs. - hybrid The control 180 162 CML333 + 184 176 fourteen* eleven* CML333- 179 165 CML322 + 185 182 twenty* 23 * CML322- 183 159 Cateto + 214 168 6 * eighteen* Cateto- 180 150 Confite + 191 170 8* 13* Confite- 189 157 Tuxpeno + 195 175 13* 10* Tuxpeno- 159 165 * indicates value p <0.05

Example 8

NP2460 × (NP2391 × CML333)

The NP2391 was crossed with CML333, and the offspring obtained from this crossing was crossed back with NP2391 for five generations to create a hybrid NP2391 × CML333 shaggy. The NP2391 × CML333 shaggy hybrid was self-pollinated for two generations, and two lines were selected based on their genotype at positions 4979-4981 of SEQ ID NO: 7: one line with the homozygous genotype CML333 (AA) ("CML333 homozygous +") and the other line with homozygous genotype NP2931 (GG) ("CML333 homozygous -"). See figure 2. Each of these lines was crossed with NP2460 to create a hybrid F1. See figure 2.

As shown in table 2, the line of the hybrid F1, created by crossing NP2460 with a line containing AA at positions 4979-4981 of the sequence SEQ ID NO: 7 ("CML333 +"), showed increased drought resistance compared with both the control hybrid and the hybrid F1 obtained by crossing NP2460 with a line containing GG at positions 4979-4981 of the sequence SEQ ID NO: 7 ("CML333-"). When treated with the stressful effects of drought, the CML333 + hybrid showed significantly higher grain yields at a standard percentage of moisture (176 bushel / acre) than both the control hybrid (162 bushel / acre) and the CML333 hybrid (165 bushel / acre).

Example 9

NP2460 × (NP2391 × CML322)

The NP2391 was crossed with CML322, and the offspring obtained from this crossing was crossed back with NP2391 for five generations to create an NP2391 × CML322 shaggy hybrid. The NP2391 × CML322 shaggy hybrid was self-pollinated for two generations, and two lines were selected based on their genotype at positions 4979-4981 of SEQ ID NO: 7: one line with the homozygous genotype CML322 (AA) ("CML322 homozygous +") and the other line with homozygous genotype NP2931 (GG) ("CML322 homozygous -"). See figure 3. Each of these lines was crossed with NP2460 to create a hybrid F1. See figure 3.

As shown in table 2, the line of the hybrid F1, created by crossing NP2460 with a line containing AA at positions 4979-4981 of the sequence SEQ ID NO: 7 ("CML322 +"), showed increased drought resistance compared to both the control hybrid and the hybrid F1 obtained by crossing NP2460 with a line containing GG at positions 4979-4981 of the sequence SEQ ID NO: 7 ("CML322-"). When treated with the stressful effects of drought, the CML322 + hybrid showed significantly higher grain yields at a standard percentage of moisture (182 bushel / acre) than both the control hybrid (162 bushel / acre) and the CML322- hybrid (159 bushel / acre). It is noteworthy that the grain yield of the CML322 + hybrid under drought conditions was almost identical to its yield under optimal conditions.

Example 10

NP2460 × (NP2391 × Cateto SP VII)

The NP2391 was mated to Cateto SP VII, and the offspring obtained from this mating was mated back to NP2391 for five generations to create a hybrid NP2391 × Cateto SP VII shaggy. The NP2391 × Cateto SP VII shaggy hybrid was self-pollinated for two generations, and two lines were selected based on their genotype at position 4641 of SEQ ID NO: 7: one line with the homozygous genotype Cateto SP VII (AA) ("Cateto homozygous +") and another line with the homozygous genotype NP2931 (GG) ("Cateto homozygous -"). See figure 4. Each of these lines was crossed with NP2460 to create a hybrid F1. See figure 4.

As shown in table 2, the line of the hybrid F1, created by crossing NP2460 with a line containing AA at position 4641 of the sequence SEQ ID NO: 7 ("Cateto +"), showed increased drought resistance compared to both the control hybrid and the hybrid F1 obtained crossing NP2460 with a line containing GG at position 4641 of the sequence SEQ ID NO: 7 ("Cateto-"). When treated with the stressful effects of drought, the Cateto + hybrid showed significantly higher grain yields at a standard percentage of moisture (168 bushel / acre) than both the control hybrid (162 bushel / acre) and the Cateto- hybrid (150 bushel / acre).

Example 11

NP2460 × (NP2391 × Confite Morocho AYA 38)

The NP2391 was mated with Confite Morocho AYA 38, and the offspring obtained from this mating was mated back to NP2391 for five generations to create the NP2391 × Confite Morocho AYA 38 shaggy hybrid. Hybrid NP2391 × Confite Morocho AYA 38 shaggy self-pollinated for two generations, and two lines were selected based on their genotype at position 4641 of SEQ ID NO: 7: one line with the homozygous genotype Confite Morocho AYA 38 (AA) ("Confite homozygous + ") and another line with the homozygous genotype NP2931 (GG) (" Confite homozygous- "). See figure 5. Each of these lines was crossed with NP2460 to create a hybrid F1. See figure 5.

As shown in table 2, the line of the hybrid F1, created by crossing NP2460 with a line containing AA at position 4641 of the sequence SEQ ID NO: 7 ("Confite +"), showed increased drought resistance compared to both the control hybrid and the hybrid F1 obtained crossing NP2460 with a line containing GG at position 4641 of the sequence SEQ ID NO: 7 ("Confite-"). When treated with the stressful effects of drought, the Confite + hybrid showed significantly higher grain yields at a standard percentage of moisture (170 bushel / acre) than both the control hybrid (162 bushel / acre) and the Confite- hybrid (157 bushel / acre).

Example 12

NP2460 × (NP2391 × Tuxpeno VEN 692)

The NP2391 was mated to Tuxpeno VEN 692, and the offspring obtained from this mating was mated back to NP2391 for five generations to create the NP2391 × Tuxpeno VEN 692 shaggy hybrid. Hybrid NP2391 × Tuxpeno VEN 692 shaggy self-pollinated for two generations, and two lines were selected based on their genotype at position 4641 of SEQ ID NO: 7: one line with the homozygous genotype Tuxpeno VEN 692 (AA) ("Tuxpeno homozygous +") and another line with the homozygous genotype NP2931 (GG) ("Tuxpeno homozygous -"). See figure 7. Each of these lines was crossed with NP2460 to create a hybrid F1. See figure 7. As shown in table 2, the line of the hybrid F1, created by crossing NP2460 with a line containing AA at position 4641 of the sequence SEQ ID NO: 7 ("Tuxpeno +"), showed increased drought resistance compared to both the control hybrid and with an F1 hybrid obtained by crossing NP2460 with a line containing GG at position 4641 of the sequence SEQ ID NO: 7 ("Tuxpeno-"). When treated with the stressful effects of drought, the Tuxpeno + hybrid showed significantly higher grain yields at a standard percentage of moisture (175 bushel / acre) than both the control hybrid (162 bushel / acre) and the Tuxpeno- hybrid (165 bushel / acre).

Example 13

Harvesting Water-Optimized Hybrids

157 water-optimized hybrids based on 36 source genotypes were compared with the base genetic (control) plant in 9-21 locations, each with four types of environment: full irrigation, limited irrigation, rainfed (no stress / adequate rainfall), rainfed stress , dry land (low plant density; no stress / adequate rainfall) and stress due to drought). As shown in tables 11 and 12, hybrids with optimized water consumption surpassed closely related basic hybrids under all conditions tested.

Table 11 Yield under full irrigation Wo Base Wo Base Difference Value hybrid haplotype * hybrid haplotype hybrid hybrid P Chia Ci 219.8 205.4 14.3 0.108 aCGhI Cgi 216.4 205.4 10.9 0.220 bCdeghil Cdeghi 224.5 213.5 11.0 0.048 average 220.2 208.1 12.1 SD 4.1 4.7 1.9 bCdefGhil CdefGh ⁽¹⁾ 241.0 226.8 14.2 0.005 bCdefGhil CdefGh ⁽²⁾ 238.0 226.8 11.2 0.030 Cefh cgi 204.4 192.1 12.3 0.077 Cefh cgi 211.2 192.1 19.2 0.018 average 223.7 209.4 14.2 SD 18.6 20.0 3.5 *: Haplotype designations refer to AM haplotypes described above. Uppercase letters indicate that the hybrid was homozygous for the corresponding haplotype, and lowercase letters indicate that the hybrid was heterozygous for the corresponding haplotype. The absence of the letter from the list AM in the designation indicates that the hybrid did not possess this haplotype.
^{(1), (2)} indicate that these plants were obtained from the same initial dilution, but were separate individual plants.

Table 12 Yield under limited irrigation WO hybrid haplotype * Basic hybrid haplotype Wo hybrid Base hybrid Difference P value Chia Ci 138.3 132.6 5.9 0.371 aCGhI Cgi 145.9 132.6 13.3 0.039 bCdeghil Cdeghi 149.2 142.1 7.2 0.266 average 144.5 135.8 8.8 SD 5.5 5.5 4.0 *: Haplotype designations as in table 11.

Table 13 Yield under stress due to drought WO hybrid haplotype * Basic hybrid haplotype Wo hybrid Base hybrid Difference P value bCdgil Cdgi 100.5 86.8 13.7 0.387 aCeGHI Ceghi 107.5 88.5 19.0 0.178 aCeGHI Ceghi 99.7 88.5 11.2 0.334 cdefGhijkl dfGh 109.3 90.9 18.4 0.157 cdefghl d 116.2 86.0 30.2 0.161 acghi cgi 102.2 81.5 20.7 0.066 acghi cgi 108.9 81.5 27.4 0.036 cefGhi cgi 96.9 77.7 19.2 0.100 cdfghe cd 95.2 81.6 13.6 0.201 average 104.1 84.8 19.3 SD 6.8 4.4 6.3 *: Haplotype designations as in table 11.

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It should be borne in mind that various details of the subject matter disclosed herein may be changed without departing from the scope of the subject matter disclosed herein. Additionally, the above description is intended for purposes of illustration only and not for purposes of limitation.

Claims (14)

1. A method of obtaining a hybrid plant Zea mays with improved optimization of water consumption, the method includes:
(a) providing a first Zea mays plant containing a first genotype containing any of the AM haplotypes;
(b) providing a second Zea mays plant containing a second genotype containing any of haplotypes AM, wherein the second plant contains at least one of haplotypes AM that is not present in the first plant;
(c) crossing the first plant and the second corn plant to obtain generation F1; and
(d) the identification of one or more representatives of the F1 generation, which contains the desired genotype containing any combination of haplotypes A-M, and the desired genotype is different from both the first genotype (a) and the second genotype (b), thereby obtaining a hybrid plant with improved optimization of water consumption,
wherein said haplotypes are defined as follows:
i) haplotype A contains nucleotide G at a position that corresponds to position 115 of the sequence SEQ ID NO: 1, nucleotide A at the position that corresponds to position 270 of the sequence SEQ ID NO: 1, nucleotide T at the position that corresponds to position 301 of the sequence SEQ ID NO: 1 : 1, and nucleotide A at the position that corresponds to position 483 of the sequence SEQ ID NO: 1 on chromosome 8 in the genome of the first plant;
ii) haplotype B contains a deletion at positions 4497-4498 of the sequence SEQ ID NO: 7, nucleotide G at the position corresponding to position 4505 of the sequence SEQ ID NO: 7, nucleotide T at the position corresponding to position 4609 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4792 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4836 of the sequence SEQ ID NO: 7, nucleotide C in a position that matches the positions and 4844 of SEQ ID NO: 7, nucleotide G at a position that corresponds to position 4969 of SEQ ID NO: 7, and TCC trinucleotide at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7 on chromosome 8 in the genome of the first plant ;
iii) haplotype C contains nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 8, nucleotide G at the position that corresponds to position 390 of the sequence SEQ ID NO: 8, and nucleotide A at the position that corresponds to position 477 of the sequence SEQ ID NO: 8 on chromosome 2 in the genome of the first plant;
iv) haplotype D contains nucleotide G at the position that corresponds to position 182 of the sequence SEQ ID NO: 19, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 330 of the sequence SEQ ID NO: 19 : 19, and nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19 on chromosome 8 in the genome of the first plant;
v) haplotype E contains nucleotide C at a position that corresponds to position 61 of the sequence SEQ ID NO: 21, nucleotide C at a position that corresponds to position 200 of the sequence SEQ ID NO: 21, and a deletion of nine nucleotides at positions that correspond to positions 316-324 the sequence of SEQ ID NO: 21 on chromosome 5 in the genome of the first plant;
vi) haplotype F contains nucleotide G at the position corresponding to position 64 of the sequence SEQ ID NO: 27 and nucleotide T at the position corresponding to position 254 of the sequence SEQ ID NO: 27 on chromosome 8 in the genome of the first plant;
vii) haplotype G contains nucleotide C at the position corresponding to position 98 of the sequence SEQ ID NO: 28, nucleotide T at the position corresponding to position 147 of the sequence SEQ ID NO: 28, nucleotide C at the position which corresponds to position 224 of the sequence SEQ ID NO: : 28, and nucleotide T at the position that corresponds to position 496 of the sequence SEQ ID NO: 28 on chromosome 9 in the genome of the first plant;
viii) haplotype H contains nucleotide T at a position that corresponds to position 259 of the sequence SEQ ID NO: 30, nucleotide T at the position that corresponds to position 306 of the sequence SEQ ID NO: 30, nucleotide A at the position that corresponds to position 398 of the sequence SEQ ID NO : 30, and nucleotide C at the position that corresponds to position 1057 of the sequence SEQ ID NO: 30 on chromosome 4 in the genome of the first plant;
ix) haplotype I contains nucleotide C at a position that corresponds to position 500 of the sequence SEQ ID NO: 36, nucleotide G at the position that corresponds to position 568 of the sequence SEQ ID NO: 36, and nucleotide T at the position that corresponds to position 698 of the sequence SEQ ID NO: 36 on chromosome 6 in the genome of the first plant;
x) haplotype J contains nucleotide A at the position that corresponds to position 238 of the sequence SEQ ID NO: 42, a deletion of nucleotides that correspond to positions 266-268 of the sequence SEQ ID NO: 42, and nucleotide C at the position that corresponds to position 808 of the sequence SEQ ID NO: 42 in the genome of the first plant;
xi) haplotype K contains nucleotide C at the position that corresponds to position 166 of the sequence SEQ ID NO: 49, and nucleotide A at the position that corresponds to position 224 of the sequence SEQ ID NO: 49, nucleotide G at the position that corresponds to position 650 of the sequence SEQ ID NO: 49, and nucleotide G at the position that corresponds to position 892 of the sequence SEQ ID NO: 49 on chromosome 8 in the genome of the first plant;
xii) haplotype L contains nucleotide C at positions that correspond to positions 83, 428, 491 and 548 of the sequence SEQ ID NO: 53 on chromosome 9 in the genome of the first plant, and
xiii) haplotype M contains nucleotide C at the position that corresponds to position 83 in the sequence of SEQ ID NO: 400, nucleotide A at the position that corresponds to position 119 of the sequence SEQ ID NO: 400, and nucleotide T at the position that corresponds to position 601 of the sequence SEQ ID NO: 400. 2. The method according to claim 1, in which the hybrid plant with improved optimization of water consumption contains one of the haplotypes AM that are present in the first plant, as well as at least one additional haplotype selected from the haplotypes AM that is present in the second the plant. 3. The method of claim 1, wherein the first plant is a recurrent parent containing at least one of haplotypes AM, and the second plant is a donor that contains at least one of haplotypes AM that is not present in the first plant. 4. The method according to p. 3, in which the first plant is homozygous for at least two, three, four or five haplotypes AM. 5. The method according to p. 3, in which the hybrid plant contains at least three, four, five, six, seven, eight or nine haplotypes AM. 6. The method according to claim 1, in which the identification includes genotyping one or more representatives of the F1 generation, obtained by crossing the first plant and the second plant, in relation to each of the haplotypes AM present in the first plant or in the second plant. 7. The method according to p. 1, in which the improved optimization of water consumption gives an increased or stable yield in the environment subjected to water stress, compared with the control plant. 8. The method according to claim 1, in which the hybrid with improved optimization of water consumption can be sown with a higher density of sowing. 9. The method according to p. 1, in which the hybrid with improved optimization of water consumption does not result in yield-related genes linking at favorable moisture levels. 10. A non-varietal inbred or hybrid plant Zea mays, the genome of which contains at least three, four, five, six, seven, eight, or nine haplotypes from haplotypes A-M, and haplotypes A-M are associated with optimization of water consumption and are defined as follows way:
i) haplotype A contains nucleotide G at a position that corresponds to position 115 of the sequence SEQ ID NO: 1, nucleotide A at the position that corresponds to position 270 of the sequence SEQ ID NO: 1, nucleotide T at the position that corresponds to position 301 of the sequence SEQ ID NO: 1 : 1, and nucleotide A at the position that corresponds to position 483 of the sequence SEQ ID NO: 1 on chromosome 8 in the genome of the first plant;
ii) haplotype B contains a deletion at positions 4497-4498 of the sequence SEQ ID NO: 7, nucleotide G at the position corresponding to position 4505 of the sequence SEQ ID NO: 7, nucleotide T at the position corresponding to position 4609 of the sequence SEQ ID NO: 7, nucleotide A at the position that corresponds to position 4641 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4792 of the sequence SEQ ID NO: 7, nucleotide T at the position that corresponds to position 4836 of the sequence SEQ ID NO: 7, nucleotide C in a position that matches the positions and 4844 of SEQ ID NO: 7, nucleotide G at a position that corresponds to position 4969 of SEQ ID NO: 7, and TCC trinucleotide at a position that corresponds to positions 4979-4981 of SEQ ID NO: 7 on chromosome 8 in the genome of the first plant ;
iii) haplotype C contains nucleotide A at a position that corresponds to position 217 of the sequence SEQ ID NO: 8, nucleotide G at the position that corresponds to position 390 of the sequence SEQ ID NO: 8, and nucleotide A at the position that corresponds to position 477 of the sequence SEQ ID NO: 8 on chromosome 2 in the genome of the first plant;
iv) haplotype D contains nucleotide G at the position that corresponds to position 182 of the sequence SEQ ID NO: 19, nucleotide A at the position that corresponds to position 309 of the sequence SEQ ID NO: 19, nucleotide G at the position that corresponds to position 330 of the sequence SEQ ID NO: 19 : 19, and nucleotide G at the position that corresponds to position 463 of the sequence SEQ ID NO: 19 on chromosome 8 in the genome of the first plant;
v) haplotype E contains nucleotide C at a position that corresponds to position 61 of the sequence SEQ ID NO: 21, nucleotide C at a position that corresponds to position 200 of the sequence SEQ ID NO: 21, and a deletion of nine nucleotides at positions that correspond to positions 316-324 the sequence of SEQ ID NO: 21 on chromosome 5 in the genome of the first plant;
vi) haplotype F contains nucleotide G at the position corresponding to position 64 of the sequence SEQ ID NO: 27 and nucleotide T at the position corresponding to position 254 of the sequence SEQ ID NO: 27 on chromosome 8 in the genome of the first plant;
vii) haplotype G contains nucleotide C at the position corresponding to position 98 of the sequence SEQ ID NO: 28, nucleotide T at the position corresponding to position 147 of the sequence SEQ ID NO: 28, nucleotide C at the position which corresponds to position 224 of the sequence SEQ ID NO: : 28, and nucleotide T at the position that corresponds to position 496 of the sequence SEQ ID NO: 28 on chromosome 9 in the genome of the first plant;
viii) haplotype H contains nucleotide T at a position that corresponds to position 259 of the sequence SEQ ID NO: 30, nucleotide T at the position that corresponds to position 306 of the sequence SEQ ID NO: 30, nucleotide A at the position that corresponds to position 398 of the sequence SEQ ID NO : 30, and nucleotide C at the position that corresponds to position 1057 of the sequence SEQ ID NO: 30 on chromosome 4 in the genome of the first plant;
ix) haplotype I contains nucleotide C at a position that corresponds to position 500 of the sequence SEQ ID NO: 36, nucleotide G at the position that corresponds to position 568 of the sequence SEQ ID NO: 36, and nucleotide T at the position that corresponds to position 698 of the sequence SEQ ID NO: 36 on chromosome 6 in the genome of the first plant;
x) haplotype J contains nucleotide A at the position that corresponds to position 238 of the sequence SEQ ID NO: 42, a deletion of nucleotides that correspond to positions 266-268 of the sequence SEQ ID NO: 42, and nucleotide C at the position that corresponds to position 808 of the sequence SEQ ID NO: 42 in the genome of the first plant;
xi) haplotype K contains nucleotide C at the position that corresponds to position 166 of the sequence SEQ ID NO: 49, and nucleotide A at the position that corresponds to position 224 of the sequence SEQ ID NO: 49, nucleotide G at the position that corresponds to position 650 of the sequence SEQ ID NO: 49, and nucleotide G at the position that corresponds to position 892 of the sequence SEQ ID NO: 49 on chromosome 8 in the genome of the first plant;
xii) haplotype L contains nucleotide C at positions that correspond to positions 83, 428, 491 and 548 of the sequence SEQ ID NO: 53 on chromosome 9 in the genome of the first plant. 11. The non-varietal inbred or hybrid plant Zea mays according to claim 10, which contains a genome containing haplotypes C, D and G; haplotypes C, D and L; haplotypes C, G, H; haplotypes C, G and I; haplotypes C, I and L; haplotypes E, G and I; haplotypes F, G and H; haplotypes A, C, F and G; haplotypes C, E, H and I; haplotypes C, G, H and I; haplotypes C, H, I and K; haplotypes C, H, I and L; haplotypes E, F, G and H; haplotypes A, C, G, H and I; haplotypes B, C, D, G and L; haplotypes C, E, G, H and I; haplotypes C, G, H, I and L; haplotypes A, C, G, H, I and K; and haplotypes C, E, F, G, H, I, J, K and L. 12. The non-varietal inbred or hybrid Zea mays plant according to claim 10, which is a hybrid plant that is homozygous for at least one of AM haplotypes. 13. The non-varietal inbred or hybrid plant Zea mays according to claim 10, which further comprises a transgene that encodes a gene product that provides resistance to a herbicide selected from glyphosate, sulfonylurea, imidazolinion, dicamba, glufisinate, phenoxypropionic acid, cyclosgecomonitrile, triaz and broxinyl. 14. A non-varietal Zea mays plant with improved optimization of water consumption, the germplasm of which includes an allele of a locus associated with a sign of optimization of water consumption, wherein this allele contains a nucleotide sequence that is at least 90% identical to any sequence SEQ ID NO: 1-117 , 400 and 401.

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