EP1006781A1 - Soja possedant des genes epistatiques influencant le rendement - Google Patents

Soja possedant des genes epistatiques influencant le rendement

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Publication number
EP1006781A1
EP1006781A1 EP98920117A EP98920117A EP1006781A1 EP 1006781 A1 EP1006781 A1 EP 1006781A1 EP 98920117 A EP98920117 A EP 98920117A EP 98920117 A EP98920117 A EP 98920117A EP 1006781 A1 EP1006781 A1 EP 1006781A1
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EP
European Patent Office
Prior art keywords
locus
linked
modifying
quantitative trait
soybean plant
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EP98920117A
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German (de)
English (en)
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EP1006781A4 (fr
Inventor
Karl G. Lark
James Orf
Kevin Chase
Fred Adler
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University of Utah
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University of Utah
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/54—Leguminosae or Fabaceae, e.g. soybean, alfalfa or peanut
    • A01H6/542—Glycine max [soybean]
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
    • A01H5/10—Seeds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • QTL quantitative trait locus
  • Molecular markers are a type of phenotype which can be detected by molecular techniques such as hybridization to a labeled DNA probe.
  • Types of molecular markers include RFLP (restriction fragment length polymorphism) , SSR (simple sequence repeat) markers , isozyme markers and the like.
  • markers provide two additional operational advantages. First, since they exist as features of the plant DNA itself, they can be detected soon after germination, for example by analysis of leaf DNA of seedlings. Selection for plants carrying the marker can be performed at the seedling stage, thereby saving the space and energy formerly needed to grow large numbers of plants to maturity. Second, molecular markers do not depend on gene expression for detection. Their use is unlikely to lead to misleading results, such as can occur when environmental or other variables modify expression of conventional marker genes.
  • Rl recombinant inbred
  • An Rl population is begun by a cross between two parent inbred (homozygous) cultivars.
  • the cultivars are preferably chosen so that a large amount of allelic variation exists between them. Only those molecular markers that are polymorphic between the two cultivars, i.e. , have a distinguishable difference between the two cultivars, can be used. Therefore, the greater the overall allelic variation between cultivars, the greater will be the number of usable molecular markers.
  • the individual progeny of the first cross are then selfed for several generations. The selfing process occurs naturally in soybean, which is a self -pollinator.
  • each segregant in the Rl population can be analyzed en masse in repeated experiments measuring various traits of agronomic interest. Simultaneously, allelic variation of individual molecular markers can be determined. It should be possible, in principle, to analyze such data for correlations between specific traits and specific marker alleles and thus identify QTLs linked to marker alleles.
  • Epistasis is the genetic term used to denote situations where non-allelic genes interact non-additively to affect the expression of a phenotype.
  • Classical epistatic effects are observed, for example, between pigment genes and genes affecting pigment distribution. Where a gene for pigment synthesis is altered or inactivated, expression of a pigment distribution gene may not be observable.
  • Quantitative traits in plants are the result of interactions between multiple QTLs and the environment [Tanksley, S.O. (1993) Ann. Rev. Genet. 27:205-233]. The existence of epistasis among QTLs extends the complexity and difficulty of identifying molecular markers linked to QTLs.
  • the present invention provides a method for plant breeding to improve a quantitative trait of agronomic value.
  • the method entails identifying a molecular marker linked to a first quantitative trait locus (QTL) at least one allele of which has an effect on a quantitative trait.
  • QTL quantitative trait locus
  • the method further entails identifying a second molecular marker linked to a second locus, at least one allele of which exerts a modifying effect on expression of the trait affected by the first locus.
  • QTL quantitative trait locus
  • second locus at least one allele of which exerts a modifying effect on expression of the trait affected by the first locus.
  • the breeding process therefore results in a novel and unique plant variety distinguished from a first parent variety by having a gene that has the potential to interact to provide improvement in a trait of agronomic value, at least one allele of such a gene being contributed by a second parent variety.
  • the invention is exemplified by a variety of QTLs in soybean affecting a variety of traits of agronomic significance, including yield.
  • Rl populations were obtained from initial crosses between cultivar- 'Archer' and cultivar 'Noir 1' or between 'Archer' and cultivar 'Minsoy' or between 'Minsoy' and 'Noir,' followed by 8-10 generations of selfmg individual offspring of the initial cross.
  • two loci affecting yield were identified in an Rl population obtained from an 'Archer 7 'Noir 1 ' cross, one linked to marker
  • the 'Noir 1 ' allele of the T153a-linked modifier gene exerted a positive effect only on the 'Noir 1' allele of the Satt277-linked yield gene.
  • the 'Archer' allele of the T153a-linked modifier had no differential effect on the 'Archer' or 'Noir 1' alleles of Satt277-linked yield gene.
  • the mean yields ranged from 34.2 Bu/ac to 40.1 Bu/ac, depending upon the combination of alleles.
  • Introgression of both 'Noir 1 ' alleles into commercial varieties can therefore increase yield dramatically. The effect could be even larger than that described herein if an endogenous yield locus of the variety is more responsive to the 'Noir 1' modifier allele.
  • modifier genes frequently modify more than one trait, additional agronomic benefits can be expected from other traits upregulated by the 'Noir 1 ' modifier, whether or not the Satt277-linked QTL was present.
  • the invention therefore provides improved plant varieties exemplified by soybean in which a varietal parent has its genotype altered to include at least a modifier gene linked to the molecular marker T153a.
  • the alteration can include introgression of one or more QTLs for traits of agronomic value, each identifiable by at least one linked molecular marker.
  • a QTL identified for soybean yield linked to the molecular marker Satt277 is a QTL identified for soybean yield linked to the molecular marker Satt277.
  • the magnitude of the modifying effect of the T153a-linked gene on a QTL varies depending on the specific allele of each gene or locus. The maximum effect on yield so far observed was obtained from the combination of the 'Noir 1 ' allele of T153a and the 'Noir 1 ' allele of Satt277. Therefore, a preferred embodiment of an improved plant variety is a commercial soybean cultivar modified to carry 'Noir 1 ' alleles of both T153a- and Satt277- linked loci
  • each point represents a single plant, with its rank with respect to the measured trait on the vertical axis and its trait data plotted on the horizontal axis.
  • Fig. 1 is based on soybean yield data for an 'Archer' X 'Noir 1 ' Rl population combined from both Minnesota and Chile test graphs.
  • Fig. IA is a standard distribution graph of yield (bu/ac) on the horizontal axis vs. number of plants (vertical axis).
  • Figs. IB-IE are cumulative distribution graphs of yield (horizontal axis) graphed against the rank of each plant with respect to yield.
  • the data are graphed separately for all plants having the 'Archer' allele of marker T153a, (labeled A, graphed as horizontal strokes) and for all plants having the 'Noir 1 ' allele of market T153a (labeled B, graphed as vertical strokes).
  • the data are graphed separately for all plants having both the 'Archer' allele of T153a(A) and the 'Archer' allele of marker Satt277 (graphed as solid circles) and for all plants having both the 'Archer' allele of T153a(A) and 'Noir 1 ' allele of Satt277 (graphed as open circles).
  • Fig. IC the data are graphed separately for all plants having both the 'Archer' allele of T153a(A) and the 'Archer' allele of marker Satt277 (graphed as solid circles) and for all plants having both the 'Archer' allele of T153a(A) and 'Noir 1
  • Fig. 2 is based on soybean yield data of the same Rl population from a Chile field test only.
  • Fig. 2 A is a conventional distribution curve of all plants.
  • Figs. 2B-E are cumulative distribution curves.
  • A designates plants having the 'Archer' T153a allele
  • B designates all plants having 'Noir 1' T153a allele
  • "a” designates plants having the 'Archer' Satt277 allele
  • "b” designates plants having the 'Noir 1 ' Satt277 alleles.
  • Plants having a particular combination of alleles are designated by a combination of upper case and lower case letters, Aa. Ab, Ba or Bb.
  • Fig. 3 is based on yield data from a 1996 Minnesota field test of the same Rl population.
  • Fig. 3 A is a conventional distribution graph for all plants.
  • Figs. 3B-E are cumulative distribution curves. All allelic designations are the same as for Figs. 1 and 2.
  • Fig. 4 is based on yield data from a 1997 Minnesota field test of the same Rl population.
  • Fig. 4 A is a conventional distribution graph for all plants.
  • Figs. 4B-E are cumulative distribution curves. All allelic designations are the same as for Figs. 1-3.
  • Fig. 5 is a graph showing the relationship between Additive Log likelihood ratio (LLR) and probability (p) values.
  • Fig. 6 is a bar graph of additive LLR values in interaction affecting yield of various marker loci in combination with marker Satt277.
  • Fig. 7 A-D shows cumulative distribution curves for seed protein content (percent by weight on a 13% water basis) in a 'Minsoy' X 'Archer' recombinant inbred population.
  • Upper case letters designate marker Sat-001, lower case designates marker SattOOl.
  • a (or a) designates an 'Archer' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 7A A is shown as horizontal strokes, B as vertical strokes.
  • Fig. 8 A-D shows cumulative distribution curves for yield (bushels/acre) in a 'Minsoy' X 'Noir 1' recombinant inbred population.
  • Upper case marker Satt365
  • Lower case marker Satt567
  • a (or a) 'Noir 1' allele
  • B (or b) 'Minsoy' allele.
  • Fig. 9 A-D shows cumulative distribution curves for seed weight (mg/seed) in a
  • Fig. 10 A-D shows cumulative distribution curves for oil content (g/kg seed on 13% water basis) in a 'Minsoy' X 'Archer' recombinant inbred population.
  • Upper case letters designate alleles of marker Sat_039
  • lower case letters designate alleles of marker Satt281.
  • a (or a) designates an 'Archer' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 11 A-D shows cumulative distribution curves for reproductive period (days) in a 'Minsoy' X 'Archer' recombinant inbred population.
  • Upper case letters designate alleles of marker Satt256
  • lower case letters designate alleles of marker Sat_112.
  • a (or a) designates a 'Noir 1' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. IID a - horizontal strokes, b - vertical strokes.
  • Fig. 12A-D shows cumulative distribution curves for oil content (g/Ug seed on a 13T water basis) in a 'Minsoy' X 'Archer' recombinant inbred population.
  • Upper case letters designate alleles of marker Satt346, lower case letters designate alleles of marker Satt372B.
  • a (or a) designates an 'Archer' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 12A, A horizontal strokes
  • B vertical strokes.
  • Fig. 12B, Aa filled circles
  • Ab open circles.
  • Fig. 13 A-D shows cumulative distribution curves for yield (bu/ac) in a 'Minsoy' X 'Archer' recombinant inbred population.
  • Upper case letters designate alleles of marker
  • Fig. 14A-D shows cumulative distribution curves for reproductive period (days), in a
  • Fig. 15 A-D shows cumulative distribution curves for leaf area (cm 2 ) in a 'Minsoy' X 'Noir 1' recombinant inbred population.
  • Upper case letters designate alleles of marker Satt066, lower case letters designate alleles of marker SattlOO.
  • a (or a) designates a 'Noir 1' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 15A, A horizontal strokes, B - vertical strokes.
  • Fig. 16 A-D shows cumulative distribution curves for flowering time (days) in an 'Archer' X 'Minsoy' recombinant inbred population.
  • Upper case letters designate alleles of marker Satt082, lower case letters designate alleles of marker R079.
  • a (or a) designates an 'Archer' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 17 A-D shows cumulative distribution curves for flowering time (days) in a 'Noir 1' X 'Minsoy' recombinant inbred population.
  • Upper case letters designate alleles of marker Satt079
  • lower case letters designate alleles of marker Sat_003.
  • a (or a) designates a 'Noir 1' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 17B, Aa filled circles, Ab- open circles.
  • Fig. 17C Ba - filled squares, Bb - open squares.
  • B vertical strokes.
  • Fig. 17B, Aa filled circles, Ab- open circles.
  • Fig. 17C Ba - filled squares, Bb - open squares.
  • FIG. 18A-D shows cumulative distribution curves for time to maturity divided by height (days/cm) in a 'Noir 1' X 'Minsoy' recombinant inbred population.
  • Upper case letters designate alleles of marker KOllc
  • lower case letters designate alleles of marker Satt307.
  • a (or a) designates a 'Noir 1' allele
  • B (or b) designates a 'Minsoy' allele.
  • Fig. 18B, Aa filled circles, Ab- open circles.
  • Fig. 18C Ba - filled squares, Bb - open squares.
  • Quantitative Trait - a trait which displays a continuous range of variation over a number of different plant varieties.
  • the variation is considered to be affected by a plurality of genes.
  • the genes controlling quantitative traits are considered to control incremental changes of the variation, and may interact with one another.
  • quantitative traits can have an effect that is only indirectly related to their primary function.
  • a gene controlling the length of maturation time can also be identified as affecting plant height, since the plant will continue to grow throughout the maturation period.
  • Environmental interactions also play an important part in measurement of a quantitative trait. For example, a trait such as yield will be affected by a trait of nematode resistance, in nematode-containing soils.
  • QTL Quantitative Trait Locus
  • Linkage is defmed by classical genetics to describe the relationship of traits which co- segregate through a number of generations of crosses. Genetic recombination occurs with an assumed random frequency over the entire genome. Genetic maps are constructed by measuring the frequency of recombination between pairs of traits or markers. The closer the traits or markers lie to each other on the chromosome, the lower the frequency of recombination, the greater the degree of linkage. Traits or markers are considered herein to be linked if there is less than 1/10 probability of recombination per generation. A 1/100 probability of recombination is defmed as a map distance of 1.0 centiMorgan (l.OcM).
  • Molecular marker is a term used to denote a DNA sequence feature which is sufficiently unique to characterize a specific locus on the genome. Examples include restriction fragment length polymorphisms (RFLP) and single sequence repeats (SSR). RFLP markers occur because any sequence change in DNA, including a single base change, insertion, deletion or inversion, can result in loss (or gain) of a restriction endonuclease recognition site. The size and number of fragments generated by one such enzyme is therefore altered. A probe which hybridizes specifically to DNA in the region of such an alteration can be used to rapidly and specifically identify a region of DNA which displays allelic variation between two plant varieties. SSR markers occur where a short sequence displays allelic variation in the number of repeats of that sequence.
  • RFLP restriction fragment length polymorphisms
  • SSR single sequence repeats
  • PCR polymerase chain reaction
  • PCR-generated fragment size can be detected by gel electrophoresis .
  • Other types of molecular markers are known. All are used to define a specific locus on the soybean genome. Large numbers of these have been mapped. Each marker is therefore an indicator of a specific segment of DNA, having a unique nucleotide sequence. The map positions provide a measure of the relative positions of particular markers with respect to one another.
  • Varietal parent is a term used herein to denote one of two parents of a crossing program intended to introduce a specific locus into a commercial variety.
  • Various commercial varieties have been developed for optimal performance under specific climate and soil conditions. Often it will be the case that new genes are to be introduced from an extraneous non-adapted or non-commercial line into an existing commercial variety. Through repeated backcrossing and selection the desired loci can be introgressed into the commercial variety while retaining most of the genetic background and performance characteristics of the commercial variety.
  • the variety into which the new genes or loci are to be introduced is termed the varietal parent herein.
  • the variety, line or strain from which the new genes or loci are derived is termed the donor variety. For example, a donor strain can be a non-commercial inbred such as Noir 1.
  • Agronomic trait is used herein as generally understood in the art to refer to traits or trait combinations which have the effect of making a plant variety valuable as a crop .
  • agronomic traits include crop yield , pathogen resistance , insect resistance , drought tolerance, nematode resistance, resistance to lodging and various adaptations to different climate and soil environments such as early maturity for northern climates, heat tolerance for southern climates , and various market-driven qualities such as seed protein content, oil content, color, flavor and the like.
  • Desirable agronomic traits can be expressed as ratios of quantitative traits as for example maturity /height, yield/height, yield/maturity, height/maturity and the like.
  • the populations included more than 230 plants.
  • Molecular mapping included more than 400 markers, of which about 300 were SSR markers and the remainder were RFLP markers. Mapping covered at least 2200 cM, including 22 linkage groups. Maps of the 'Archer' X 'Noir,' 'Archer' X 'Minsoy' and 'Minsoy' X 'Noir 1 ' populations are shown in Table 1. The Rl populations were planted in fields in
  • the 'Archer' X 'Noir 1 ' Rl population was screened generally for QTLs and concurrently mapped using RFLP and SSR markers, essentially as described previously for a 'Minsoy' x 'Noir 1 ' Rl population [Lark, K.G. et al. (1993) Theor. Appl. Genet. . 86:901-906, incorporated herein by reference; Mansur et al. (1993); Mansur et al (1996)]. Markers were analyzed by standard methods, such as described, e.g., by Mansur et al. (1996). Map positions for markers were determined by internal mapping [Lander et al.
  • LLR log likelihood ratio
  • An additive LLR was calculated to evaluate the likelihood that the observed effects of two loci in a specific allelic combination deviated from an assumed additive effect of all combinations of the two loci. The calculations were also based on the assumption that the data are normally distributed, and that the variances are given by the uncorrected sample variances, for example:
  • A, B, refer to alleles of the first locus and a, b refer to alleles of the second locus; and T denotes the total population. Subscripts denote sub-populations corresponding to the genotypes in question.
  • n A number of plants in the A group
  • a and B were used to denote different alleles of a given locus. For example at the
  • T153a linked locus A represents the 'Archer' allele
  • B represents the 'Noir 1 ' allele.
  • An unlinked second locus allele was denoted by lower case letters, e.g. at Satt277, a denotes the 'Archer' allele and b denotes the 'Noir 1 ' allele (See Fig. 1).
  • Each designated subgroup includes all tested plants of the Rl population which carry the designated allele or combination of alleles.
  • LLR values are natural logarithms of d e likelihood ratios. Therefore a difference of 1 unit corresponds to a factor of about 2.718, the numerical value of e.
  • a small additive log likelihood ratio indicates that the data can be effectively explained by die additive model, while a large LLR indicates diat the data are not additive.
  • the null LLR was tested by creating random groups from the data set. The order of die total set of plants was randomized, placing the first plants arbitrarily into an A group and the remaining plants into the B group. The resulting null LLR was then calculated. After a number of trials, the p value is based on number of times LLR was exceeded total number of trials
  • the additive LLR was calculated from the randomized populations. For example, the order of the A group data was randomized and separated into two groups corresponding to the frequency of a and b genotypes. The first group was then treated as the Aa group. The remaining group became the Ab group. (Group size was allocated according to the actual group sizes of the original data). In similar fashion the order of the B-group was randomized, a first group was assigned to Ba and the remaining group to Bb.
  • Additive LLR values and p-values are related as graphically shown in Fig. 5 , assuming normal distribution of data. For example, an LLR of 9 indicates a probability of slightly greater than 10 "5 (1 in 100,000) that a random assortment of the data could yield the observed differences in trait distribution. For higher LLR values, an accurate evaluation of p requires large numbers of simulations, (as many as 100 million). The greater the LLR, or the smaller the p-value, the more significant the data. Data showing lower LLR values are less significant, so that additional tests or larger trials might fail to support conclusions drawn from me original trial. Factors which affect the LLR, and titierefore the significance of data include the following:
  • the amount of variation controlled by the locus being tested me contribution of a QTL which has only a small effect on the measured trait can be difficult to measure significantly if the effects of other QTLs predominate;
  • the reproducibility of the test genetics and environment are the two factors affecting reproducibility.
  • the genetic variation within a given Rl population is set.
  • the degree of linkage between the marker and the locus the closer me marker physically lies to the locus, the greater me likelihood of observing an effect controlled by the locus.
  • an LLR value is a physical attribute of plant DNA, representing the length of DNA that includes the marker and e QTL controlling the trait.
  • FIG. 6 where the additive LLR values are shown for a modifier locus linked to T153a whose interaction with a QTL linked to marker Satt277 is to be described below as well as in Figs. 1-4.
  • a series of markers on group U3 map at varying distance from T153a. Marker Alll maps about 15.5 cM from T153a.
  • the additive LLR for interaction with Satt277 is less than 9.
  • the marker gmenod maps 5.7 cM from T153a, with an additive LLR greater than 16.
  • the marker T153a shows a slightly greater LLR than B172, suggesting even closer linkage to the modifier locus, almough the two markers appear very close to each other by conventional mapping.
  • the seed color locus I (a conventional trait) also lies close to me modifier locus although at present not as precisely mapped as molecular markers such as B 172.
  • I and R are actual genetic loci for the trait, not marker loci.
  • the phenotypic value is higher for black seeds than for yellow or brown seeds.
  • the additive LLR measured for the interaction between I and R is 32 and represents a case where the trait was measured directly, i.e. , the marker is the trait.
  • Trait associations having high LLR values, greater than about 9 measured as described, are useful as providing identification of epistatic interactions between traits closely linked to markers.
  • the high LLR interactions are also useful for identifying cloning markers, as well as marker pairs that "bracket" the locus, i.e. , lie on either side of the locus, such that the locus can be followed, without loss during crosses.
  • Preferred marker-linked interactions are those that display an LLR greater than about 12. Even more preferred interactions are those displaying an LLR greater than about 15 The most preferred interactions display an LLR greater than about 18. To date, it is believed ti at no epistatic interactions between a modifier locus and a QTL affecting yield have been reported with an LLR greater than 9.
  • loci that modify the expression of other loci is commonplace. However, modifying loci are typically closely linked to the gene or genes they modify. If mis were not the case, trait segregation after crossing would continually separate modifier and gene so that no evolutionary change could flow from the ability to modify the gene. However, in self-pollinating plants, no such selection pressure exists to maintain linkage between interacting loci. Unlinked interacting loci are expected to be found most frequently in self-pollinating plants. The methods of the invention are therefore applicable to all self-pollinating plant species including self-pollinating crop species including, without limitation, soybean, wheat, rice, oats and barley.
  • Marker-linked QTLs and modifiers thereof can be found in any of the foregoing crops and have interactive effects with an LLR greater than about 9, preferably greater than about 12, more preferably greater than about 15 , and most preferably greater than about 18. As demonstrated herein, such interactive effects can dramatically affect yield. Similarly, effects on QTLs controlling other traits of agronomic value have been found.
  • the dark seed color of me 'Noir 1 ' cultivar has been considered an undesirable trait for commercial soybeans.
  • the I locus which controls seed coat color has been noted as lying close to the T153a-linked modifier QTL.
  • Prior breeding efforts which used 'Noir 1,' but selected to avoid black seed color would have failed to exploit the modifier locus linked to T153a. It is unlikely that the locus in its 'Noir 1 ' allelic form currently exists in most commercial, white- seeded cultivars.
  • Seedlings from the initial cross are heterozygous at the loci of interest and must be selfed in order to provide a second generation (F2 plants) in which segregation occurs and in which a portion of the plants will be homozygous at the desired locus, in accord with well- known principles of genetics.
  • F2 plants second generation
  • both alleles of the desired loci are from the same donor plant source, e.g. 'Noir,' that cultivar can be used as one parent in the cross.
  • any parent having the desired alleles can be used (for example any of the described Rl lines).
  • Progeny segregant seedlings of the cross e.g.
  • F2 plants can be analyzed as seedlings for the presence of markers linked to the desired allele, for example, an allele of the T153a-linked modifying locus, or for the presence of an allele of the Satt277-linked QTL or the simultaneous presence of particular alleles of both loci.
  • markers linked to the desired allele for example, an allele of the T153a-linked modifying locus, or for the presence of an allele of the Satt277-linked QTL or the simultaneous presence of particular alleles of both loci.
  • Those plants possessing the desired loci are selected and grown to maturity for further evaluation. Further stages of crossing, back- crossing and selfing can be carried out as will be understood in the art, with selection for the presence of each desired locus, as described.
  • desired agronomic traits including mose of the varietal parent and those contributed by the QTL and die modifying locus can be carried out at d e breeder's discretion, to obtain true-breeding progeny having me desired traits. Because most of the desired agronomic traits are already present in the varietal parent, the result of the foregoing breeding process should derive most of its genetic background from the varietal parent, with the significant addition of die desired interacting pair of loci such as a T153a-linked modifier locus and a Satt227-linked QTL affecting yield. From cumulative distribution curves such as those of Figs.
  • the 'Noir 1' alleles, the modifier locus and the QTL are the preferred alleles of these loci. Improved lines also can be developed using other alleles of these loci.
  • the foregoing breeding process combines a varietal parent (first parent) and a donor parent (second parent) and results in a novel variety having genes of the varietal parent and at least one specific locus of die donor parent. It will be understood diat the existence of otiier modifiers in the varietal parent may effect the quantity of the desired trait observed after crossing. Other effects, including "linkage drag" are well known in the art of plant breeding to result in the introduction of genes located near the desired QTL, such that trait values in the crosses may be affected. Such phenomena are recognized and well understood characteristics of plant breeding which accompany the introgression process.
  • Fig. 2 the data of Fig. 1 were subdivided to display only the yield data from the Chile field test and in Fig. 3 are shown the data for the 1996 Minnesota field test.
  • die data of Fig. 1 were subdivided to display data of die 1997 Minnesota field test.
  • the similarity of the data of Figs. 2, 3 and 4 indicate mat the environmental differences between these three tests did not contribute to die epistatic effect.
  • the additive LLR for combined Chile and Minnesota tests is much greater than eid er test alone. Therefore, despite environmental differences, the cumulative effect of the data increases the significance of the epistatic effect and underscores the magnitude of die interaction in increasing yield and me closeness of the linkage. Yield can be affected indirectly by other quantitative traits.
  • loci diat do not significantly alter other traits of agronomic importance. For example, increasing yield while also increasing plant height can be counter-productive if me taller plants are more susceptible to lodging.
  • the preferred trait is one which can be introduced into an existing commercial variety without degrading o ier aspects of agronomic performance for which the variety has been developed. The QTL linked to Satt277 does not have a significant effect on odier traits that might indirectly affect yield.
  • Table 2 summarizes field data from field tests grown in Minnesota (MN96) and in Chile (CH95) standardized to averages of all plants in the Minnesota test (std MN96).
  • LLR and p-values were calculated for die interaction of the Satt277-linked QTL and its modifier, linked to T153a.
  • the traits measured were height (HT), lodging (LD), days to maturity (R8), seed weight (SW) and yield (YD).
  • HT height
  • LD lodging
  • R8 days to maturity
  • SW seed weight
  • YiD yield
  • the modifying locus linked to T153a is also closely linked to anotiier molecular marker, B172. Both map to linkage group U3 (Table 1). A gene which modifies or regulates another gene can regulate several odier genes as well.
  • the B172- or T153a-linked regulator function can be used to effect interactions with o ier QTLs. Therefore, the modifying locus linked to B172 and/or T153a can be useful by itself in a breeding program to enhance die activity of otiier endogenous QTLs in a varietal parent.
  • Markers B172 and T153a are RFLP probes. B172 and KOllc are available from Biogenetic Services, Inc. , 2308 - 6th Street East, Brookings, SD 57006. T153a was developed in the inventors' laboratory as described by Lark et al. (1993). The sequence of the T153a RFLP probe is given in SEQ ID NO: 1 (See Table 3).
  • markers designated by a number preceded by “Satt” or “Sat” are microsattelite DNA markers isolated at die United States Department of
  • Fig. 18D shows me distributions of plants having me 'Noir 1' allele of Satt307(a) and of plants having the 'Minsoy' allele of Satt307(b). Satt307 maps to linkage group U9.
  • FIGs. 18B and 18C An interaction of die two loci is readily seen from Figs. 18B and 18C.
  • Fig. 18B plants carrying the combination of 'Noir 1' allele of KOllc and 'Minsoy' allele of Satt307 (Ab) display higher maturity /height ratios than diose having me combination of 'Noir 1 ' K01 lc and 'Noir T Satt307.
  • FIG. 18C the effect of the 'Minsoy' allele of KOllc in combination with each of ie Satt307 alleles is shown (Ba and Bb).
  • the K01 lc marker is linked to a locus which exerts a modifying effect on die QTL linked to Satt307.
  • a very large LLR of 17.5 characterizes the magnitude of die interaction.
  • FIG. 8 A-D Further examples of interactions affecting yield are shown in Fig. 8 A-D and Fig. 13A- D.
  • Fig. 8 interacting loci linked to markers Satt365 and Satt567 were identified in a 'Minsoy' X 'Noir 1 ' Rl population. Field data were obtained in a 1993 Minnesota field Test. The interaction was characterized by an LLR of 9.82.
  • a pair of loci displaying an interaction between a modifying locus and a QTL affecting seed weight was found in me 'Archer' X 'Noir 1' Rl population.
  • the marker linked to die QTL was Satt315, and die modifying locus was linked to Satt080. Cumulative distributions are shown in Fig. 9A-D.
  • the interaction is characterized by an LLR of 10.58. The data were combined from all field trials.
  • the second interaction affecting oil content was observed from field data from a 1997 Minnesota test.
  • the interacting loci were linked to markers Sat_039 and to Satt281, respectively. Cumulative distributions are shown in Fig. 10 A-D.
  • the interaction was characterized by an LLR of 10.50.
  • the reproductive period (days from flowering to maturity) was affected by interacting loci in the 'Archer' X 'Minsoy' Rl population.
  • the loci were linked to marker Satt256 and to Satt_112, respectively.
  • Data were obtained in a 1995 Minnesota field test. Cumulative distribution curves are shown in Fig. 11 A-D.
  • the interaction was characterized by an LLR of 11.44.
  • Example 11 Leaf area (cm 2 ) was affected by an interaction identified in the 'Noir 1 ' X 'Minsoy' Rl population based on data obtained in a 1992 field test in Chile. The loci were linked to marker Satt066 and to marker SattlOO, respectively. Cumulative distributions are shown in Fig. 15A- D. The interaction was characterized by an LLR of 10.10.
  • interacting loci that significantly affect a variety of agronomic traits exist in plants, particularly self-pollinating plants such as soybean. Markers linked to such loci can be used in conventional plant breeding to improve or modify agronomic traits, by selecting for the combined presence of me desired alleles of the desired interacting pairs in the progeny of crosses. While the interactions have been observed in specific Rl populations, it will be understood that interacting loci are not limited to crosses with a specific line or to a specific Rl population or to a specific cross. The methods described herein can be reproducibly applied to identify interacting pairs of QTLs in any Rl line.
  • MOLECULE TYPE DNA (genomic)
  • ACCCCATCAT CCAGTACTCC ACGCTGTGCT GCTTCTTCAG 480
  • CCCCCAGTTC ACCGGCCACG CCGGCCAGTC CTCAACGGTG ACGGGCGTCT CCGACGCGCT 540

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Abstract

L'invention concerne un procédé d'amélioration de plantes appliqué aux plantes autopollinisatrices ainsi que les plantes obtenues par ce procédé. Le procédé comprend l'utilisation de marqueurs moléculaires liés aux sites actifs interagissants qui influencent les caractères ayant une valeur agronomique. Ce procédé permet d'identifier un premier marqueur moléculaire lié à un site de caractère quantitatif (QTL) et un deuxième marqueur moléculaire lié à un site modificateur qui a un effet épistatique en combinaison avec le QTL. On peut utiliser des étapes de sélection classique pour introgresser les sites interagissants dans d'autres variétés de plantes.
EP98920117A 1997-05-02 1998-05-01 Soja possedant des genes epistatiques influencant le rendement Withdrawn EP1006781A4 (fr)

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BRPI0413253B1 (pt) 2003-08-01 2015-03-03 Pioneer Hi Bred Int Método para identificar uma sublinhagem de soja com aumento de produtividade e conjunto de marcadores úteis para a identificação de uma planta de soja com aumento de produtividade
NZ552434A (en) * 2004-07-09 2010-12-24 Monsanto Technology Llc Soy compositions having improved organoleptic properties and methods of generation
EP1781821A2 (fr) 2004-08-06 2007-05-09 Pioneer Hi-Bred International, Inc. Sites actifs genetiques associes a la tolerance au phytophthora dans le soja
CA2581846C (fr) * 2004-09-29 2015-04-07 Monsanto Technology Llc Plantes de soja a rendement eleve comprenant une faible teneur en acide linolenique
CN101475939B (zh) * 2007-12-31 2012-01-18 东北农业大学 与大豆百粒重和大豆产量相关的数量遗传位点及其应用
CN101613753B (zh) * 2009-08-07 2012-06-06 中国科学院遗传与发育生物学研究所 辅助鉴定大豆百粒重相关位点的一对专用引物及其方法
US9965584B2 (en) 2011-05-17 2018-05-08 National Ict Australia Limited Identifying interacting DNA loci using a contingency table, classification rules and statistical significance
CN103320427B (zh) * 2012-03-20 2014-12-10 东北农业大学 一种辅助鉴定大豆对大豆花叶病毒抗性的方法
CN103045588B (zh) * 2012-12-11 2014-08-20 南京农业大学 大豆籽粒蛋白质含量主效qtl 的分子标记及其应用
US9493843B2 (en) 2012-12-20 2016-11-15 Pioneer Hi-Bred International, Inc. Genetic loci associated with Phytophthora tolerance in soybean and methods of use
CN108531562A (zh) * 2018-04-20 2018-09-14 青海省农林科学院 一种辅助鉴定蚕豆种皮无单宁性状的方法

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WO1997012059A1 (fr) * 1995-09-26 1997-04-03 Pioneer Hi-Bred International, Inc. Resistance a la brunissure de la tige chez les sojas

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WO1997012059A1 (fr) * 1995-09-26 1997-04-03 Pioneer Hi-Bred International, Inc. Resistance a la brunissure de la tige chez les sojas

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