WO1996011566A1 - Gene controlling floral development and apical dominance in plants - Google Patents

Abstract

The present invention provides compositions and methods for affecting the transition from vegetative to reproductive growth in a wide variety of plants. A MADS-box gene from rice, OsMADS1, has been isolated and sequenced. Expression of OsMADS1 in transgenic plants dramatically alters development, resulting in early flowering plants with reduced apical dominance, causing both long-day and short-day plants to flower under both short-day and long-day conditions. OsMADS1 is a key regulatory factor determining the transition from shoot apex to floral meristem and is a target for action of flower induction signals.

Description

GENE CONTROLLING FLORAL DEVELOPMENT AND APICAL DOMINANCE IN PLANTS

TECHNICAL HELP This invention is related to the field of compositions and methods for affecting plant floral development and more particularly to an isolated gene and its use in affecting the timing of the transition from vegetative to reproductive growth.

BACKGROUND ART A majority of plants use environmental cues to regulate the timing of the transition from vegetative to reproductive growth in order to ensure synchronous flowering for successful outcrossing and to complete their sexual reproduction under favorable conditions (reviewed in Bernier et al., Plant Cell 5:1 147-1 155, 1993). The major environmental factors that control the transition are photoperiod, temperature, and nutrition.

In responding to these environmental factors, plants differ widely among species, among cultivars within species, and among stages of plant development within a cultivar. A short-day plant flowers when the day length is less than its critical length and a long-day plant flowers when the day length is longer than its critical length. Floral induction in a day-neutral species is unaffected by day-length, but occurs when the plant has attained a minimum amount of growth. After completion of the basic vegetative phase, initiation of flowering is frequently dependent on the day length. The critical photoperiod is defined as the maximum day length that will induce a short-day plant to flower and the minimum day length that will induce a long-day plant to flower.

It has been postulated that a transmissible flowering signal is produced mainly in leaves and is transported to the shoot apex through the phloem. Grafting experiments have shown that leaves of photoperiodic plants produce promoters and inhibitors of flowering when exposed to favorable and unfavorable daylength regimes, respectively (Lang et al., Proc. Natl. Acad. Sci. USA 74:2412-2416, 1977). The nature of these transmissible signals is still controversial (O'Neill, Photochem. Photobiol. 56:789-801 , 1992) and efforts to isolate the signaling substances have been unsuccessful. In addition, the target genes for these signals in the shoot apex have not been identified.

Significant effort has been expended in attempts to elucidate the underlying mechanisms controlling flower development in various dicotyledonous plant species (reviewed in Coen, Annu. Rev. Plant Physiol. Plant Mol. Biol. 42:241 -279, 1991 ; and Gasser, Annu. Rev. Plant Physiol. Plant Mol. Biol. 42:621 -649, 1991 ), leading to the isolation of a family of genes which encode regulatory proteins. These regulatory proteins include AGAMOUS {AG) (Yanofsky et al.. Nature 346:35-39, 1990), APETELA I [API) (Mandel et al., Nature

360:273-277, 1992), and APETALA 3 IAP3) (Jack et al.. Cell 68:683-697, 1992) in Arabidopsis thaliana, and DEFICIENS A iDEFA) (Sommer et al., EMBO J. 1 1 :251-263, 1990), GLOBOSA (GLO) (Trobner et al., EMBO J.

11 :4693-4704, 1992), SQUAMOSA {SQUA) (Huijser et al.. EMBO J. 1 1 :1239-1249, 1992), and PLENA iPLE) (Bradley et al., Cell 72:85-95, 1993) in Antirrhinum majus.

Mutations in an AG or PLE gene result in homeotic alterations of the stamen and carpel. Genetic studies have shown that the DEFA, GLO and AP3 genes are essential for petal and stamen development. AP/ and SQUA genes, which are expressed in young flower primordia, are necessary for the transition of an inflorescence meristem into a floral meristem. Sequence analysis of these genes has revealed that their gene products contain a conserved MADS-box region (Bradley et al., Cell 72:85-95, 1993; Huijser et al., EMBO J. 1 1 :1239-1249, 1992; Jack et al., Cell 68:683-697, 1992; Mandel et al.. Nature 360:273-277, 1992; Sommer et al.,

EMBO J. 1 1 :251-263, 1990; Trobner et al., EMBO J. 1 :4693-4704, 1992; Yanofsky et al., Nature 346:35-39, 1990), which is probably a DNA-binding domain (Schwarz- Sommer et al., EMBO J. 1 1 :251 -263, 1992).

Using these clones as probes, MADS-box genes have been isolated from other species including tomato (Mandel et al., Cell 71 :133-143, 1992), tobacco

(Kempin et al., Plant Physiol 103:1041 -1046, 1993), petunia (Angenent et al., Plant Cell 4:983-993, 1992), Brassica napus (Mandel et al., Cell 71 :133-143, 1992), and maize (Schmidt et al., Plant Cell 5:729-737, 1993).

Transgenic approaches have been employed to study the functional roles of MADS-box genes. Genetic complementation of the ag-2 mutant by the AG gene demonstrated that the ag-2 gene product is involved in stamen and carpel development (Yanofsky et al., Nature 346:35-39, 1990). Ectopic expression of the AG genes from A. thaliana, B. napus, petunia, tobacco, and tomato resulted in homeotic conversion of sepals to carpels and petals to stamens, mirroring the ap2 mutant phenotype (Kempin et al., Plant Physiol 103:1041 -1046, 1993; Mandel et al., Cell 71 :133-143, 1992; Mizukami and Ma, Cell 71 :1 19-131 , 1992; Pnueli et al., Plant Cell 6:163-173, 1994; Tsuchimoto et al., Plant Cell 5:843-853, 1993). These results support the hypothesis that AG and AP2 act in an antagonistic fashion.

Antisense approaches have also been used to reveal the functional role of the tomato MADS-box genes (Pnueli et al., Plant Cell 6:175-186, 1994; Pnueli et al., Plant Cell 6:163-173, 1994). Transgenic plants that express tomato AG antisense RNA display the ag mutant phenotypes. Antisense expression of the tomato TM5 MADS-box gene results in morphological changes in the three inner whorls of transgenic plants.

The timing of the transition from vegetative growth to flowering is one of the most important steps in plant development. This determines quality and quantity of most crop species since the transition determines the balance between vegetative and reproductive growth. It would therefore be highly desirable to have means to affect the timing of this transition. The present invention meets this and other needs.

SUMMARY OF THE INVENTION The present invention provides compositions and methods related to the

OsMADSl gene of Oriza sativa and homologs thereof, such as the NtMADSI gene of Nicotiana tabacum and their use to alter the phenotype of a plant, including phenotypes related to the timing of the transition between vegetative and reproductive growth. It is an object of the invention to provide isolated nucleic acids comprising at least 15 contiguous nucleic acids of (1 ) a native OsMADSl gene, including alleles and homologs or (2) variants of a native OsMADSl gene, and preferably the full length native sequence of OsMADSl or NtMADS3 as shown in Figs. 1A or 10, respectively. When expressed in a transgenic plant, the OsMADSl gene produces at least one phenotype including (1 ) diminished apical dominance, (2) early flowering, (3) a partially or completely altered daylength requirement for flowering, (4) greater synchronization of flowering, or (5) a relaxed vernalization requirement. Variant forms of the OsMADSl gene are preferably substantially similar in sequence to a native OsMADSl gene and preferably comprise only silent or conservative substitutions to a native OsMADSl gene sequence.

A further object of the invention is to provide host cells and transgenic plants in which an OsMADSl gene or fragment thereof is introduced.

A further object of the invention is to provide purified polypeptides encoded by an OsMADSl nucleic acid, e.g., by expression of an expression vector comprising an OsMADSl gene or fragment thereof in a suitable host cell.

A further object of the invention is to provide probes and primers comprising a fragment of an OsMADSl gene capable of hybridizing under stringent conditions to a native OsMADSl gene sequence. Such probes and primers are useful, for example, in studying the structure and function of OsMADSl genes and for obtaining homologs of the OsMADSl gene from plants other than rice and tobacco.

The expression of an OsMADSl transgene in transgenic plants of a long- day or short-day species, as noted above, can result in day-neutral phenotype, for example. Therefore, it is a further object of the invention to use such transgenic plants to produce multiple crops in a year, which otherwise cannot be accomplished under natural photoperiod conditions.

The foregoing and other objects and advantages of the invention will become more apparent from the following detailed description and accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS Fig. 1 A shows the nucleotide and deduced amino acid sequences of OsMADSl cDNA. MADS-box and K-box regions are underlined. The positions of nucleotides and amino acids are shown on the left and right, respectively. Fig. 1 B provides a comparison of MADS-box regions, showing the alignment of the MADS-box sequence of OsMADSl (residues 2-57) with the MADS- box sequence of API, SQUA, AG, PLE, AP3, DEF A. The asterisks indicate amino acids that are identical to corresponding amino acids of OsMADSl .

Figs. 2A and 2B show the results of a Southern blot analysis of rice DNA digested with fcoRI (E), HindlW (H), or Pst (P) and hybridized with a probe prepared from the entire OsMADSl cDNA (Fig. 3A) or an OsMADSl cDNA probe lacking the conserved MADS-box region (Fig. 3B). The position of V/ru/lll-digested lambda DNA size markers is also indicated in both Figs. 2A and 2B.

Figs. 3A and 3B show the results of a Northern blot analysis of the OsMADSl transcript in rice, using as a probe a OsMADSl cDNA lacking the MADS domain. Fig. 3A specifically shows OsMADSl expression patterns in rice organs: (L) leaf, (R) root, (A) anther, (C) carpel, and (P) palea/lemma of anthesis-stage flowers. Fig. 3B shows a temporal expression pattern during flower development, wherein total RNA isolated from rice flowers at different developmental stages was used for detection of OsMADSl gene expression: 1 , young inflorescence (panicle size < 1 cm); 2, young flower (panicle size = 1 to 6 cm); 3, flower at the early vacuolated pollen stage; and 4, flower at the late vacuolated pollen stage.

Figs. 4A - 4E depict localization of the OsMADSl transcript in rice flowers and phenotypes of transgenic tobacco plants expressing OsMADSl , wherein Fig. 4A shows a young inflorescence; Figs. 4B and 4C show cross sections of upper and lower rice flowers at the vacuolated pollen stage, respectively (A, anther; F, filament; FP, flower primordia; L, lemma; 0, ovary; P, palea; S, sheath; SL, sterile lemma); Fig. 4D provides a comparison of OsMADSl transgenic plant #7 (left) and a wild-type SR1 tobacco (right); and Fig. 4E is a close-up picture of OsMADSl transgenic plant #2 showing branching and bushy phenotypes.

Fig. 5 shows the results of a northern blot analysis of OsMADSl transcripts in transgenic tobacco, using as the probe an OsMADSl cDNA lacking the MADS-box domain, wherein the "C" denotes a control plant and the numerals "1 " throυgh "7" denote seven different transgenic plants exhibiting the early flowering and dwarf phenotypes.

Fig. 6 shows phenotypes of transgenic N. sylvestris plants expressing OsMADSl . Transgenic (left) and untransformed control (right) plants grown under long-day growth condition (16 hr daylength) (Fig. 6A) or a short-day growth condition (10 hr daylength) (Fig. 6B).

Fig. 7 shows the results of a northern blot analysis of OsMADSl transcripts in transgenic N. sylvestris using as a probe an OsMADSl cDNA lacking the MADS-box domain. "1 " through "5" denote five independently transformed transgenic plants exhibiting early flowering under both permissive and non-permissive conditions. C, control untransformed control N. sylvestris.

Fig. 8 shows phenotypes of transgenic N. tabacυm cv. Maryland Mammoth plants expressing OsMADSl . Transgenic plants (left) and untransformed control (right) grown under a short-day growth condition (10 hr daylength) (Fig. 6A) or a long-day growth condition (16 hr daylength) (Fig. 6B).

Fig. 9 shows the results of a northern blot analysis of OsMADSl transcripts in transgenic N. tabacυm cv. Maryland Mammoth using as a probe an OsMADSl cDNA lacking the MADS-box domain. "1 " through "3" denote three independently transformed transgenic plants exhibiting early flowering under both permissive and non-permissive conditions. C, untransformed control N. tabacυm cv. Maryland Mammoth.

Fig. 10 shows the nucleotide and deduced amino acid sequence of the NtMADS3 cDNA. The positions of nucleotides and amino acids are shown on the left and right, respectively. Fig. 1 1 shows a nucleotide sequence comparison of the NtMADS3 cDNA

(top) with the OsMADSl cDNA (bottom). The positions of the nucleotides for each cDNA are shown on the left and right.

DETAILED DESCRIPTION OF THE INVENTION The present invention provides compositions and methods related to a "MADS-box" gene from rice, OsMADSl , and its homologs that are useful, for example, for producing dwarf plants and for affecting the timing of the transition from vegetative to reproductive growth in a wide variety of plants, including various dicotyledonous and monocotyledonous crop plants and tree species (see Schwarz- Sommer et al.. Science 250:931 -936, 1990 regarding "MADS-box" genes). OsMADSl is a key regulatory factor determining the transition from shoot apex to floral meristem and is likely a target for action of flower induction signals.

The mechanism for the function of the rice OsMADSl gene product is unknown. The OsMADSl gene product may regulate the expression of genes that are involved in the induction of flowering, thus leading to the early flowering and dwarf phenotypes observed in day-neutral plants and overriding the photoperiod requirement for flowering in flowering plants of a species that is normally daylength-sensitive (i.e., a long-day and short-day species). The OsMADSl polypeptide may, for example, act as a positive regulatory factor similar to API or SQUA. Since the 35S promoter is active in most cell types, it is likely that OsMADSl polypeptide produced under the control of the 35S promoter is accumulated in the shoot meristem and inflorescence meristem, where the AP1 (SQUA)-W B gene is not yet activated. It has been reported that at least two genes, API and LEAFY, are required for the transition of inflorescence meristem into floral meristem in Arabidopsis (Weigel et al., Cell 69:843- 859, 1992). Similarly, SQUA and FLORICAULA are required for floral organ induction in Antirrhinum ma/us (Coen et al., Cell 63:131 1-1322, 1990). It was determined that API and SQUA belong to the MADS-box gene family (Coen et al., Cell 63:131 1 -1322, 1990; Weigel et al., Cell 69:843-859, 1992). If API is normally expressed later than LEAFY, the ectopic expression of OsMADSl may bypass the transient period required for normal floral organ development. Alternatively, the OsMADSl protein may interact with a negative factor that normally inhibits flowering. It is also possible that a higher level of expression of OsMADSl may enhance the response to flower-promoting signals. No other MADS-box genes have been shown to induce early flowering and dwarfing and to override photoperiod requirements, for example. Although the early flowering and dwarf phenotypes were not apparent in transgenic plants in their juvenile state, axillary bud growth was initiated during the early stage of floral meristem development. The growing shoot apex is known to exert an influence over a range of developmental events, including axillary bud growth (Tamas, Hormonal regulation of apical dominance. In: Davies, ed., Plant Hormones and Their Role in Plant Growth and Development, Martinus Nijhoff Pub., Dordrecht, Netherlands, 1987, pp. 393-410). The effect is greatest early in plant development. As plants mature, the emergence of floral organs releases inhibition of the lateral buds and allows them to develop. The active substance responsible for apical dominance in a number of plant species has been identified as the plant growth regulator, indoleacetic acid (IAA). In transgenic plants expressing OsMADSl , the dwarf phenotype may be the result of altered hormonal status due to early flowering. Use of the OsMADSl Gene and its Homoloαs for Crop Improvement According to the present invention, the OsMADSl gene is useful, for the following purposes, among others. (Reference to the OsMADSl gene is intended to encompass alleles, homologs, and variants as well). Early flowering. The timing of the transition between vegetative and reproductive growth is an important agronomic trait, serving as a crucial factor in determining crop yields. Expression of the OsMADSl gene in transgenic plants makes it possible to affect the transition from vegetative to reproductive growth in a wide variety of plants, whether the plants are long-day, short-day, or day-neutral plants. When the OsMADSl gene is expressed in transgenic plants of day- neutral species, the resulting transgenic plants flower earlier than control plants. Transgenic long-day and short-day flowering plants expressing the OsMADSl gene also flower earlier under permissive conditions than control plants. The compositions and methods according to the present invention therefore permit one to reduce the length of the vegetative growth stage of cereal, fruit, vegetable, floricultural, and other crop species.

Producing dwarf plant varieties. Although it has been possible to enhance the harvest index in grain crops by the use of dwarfing genes, the isolation of these genes producing dwarf phenotypes has been difficult.

Transgenic plants comprising a OsMADSl transgene are shorter than controls. Expression of an OsMADSl transgene apparently causes no significant change in the rate of photosynthesis or the total mass of the plant. Therefore, the OsMADSl gene is useful for producing dwarf plant varieties for a variety of plants including cereal, fruit, and floricultural species.

Synchronizing reproductive growth. Transgenic plants expressing the OsMADSl transgene flower more synchronously than controls. Therefore, the gene can be used for crops for which synchronized harvesting is economically beneficial, allowing more effective use of mechanized harvesting of fruit species or the production of floricultural species having improved flower quality, for example. Producing dav-neutral plant varieties. Expression of an OsMADSl transgene in daylength-sensitive (i.e., long-day or short-day) plants at least partially overrides the photoperiod requirement for flowering and can completely override the photoperiod requirement. By introducing such a transgene into a wide variety of photoperiod-sensitive crop species, including, but not limited to rice and soybeans, these plants effectively become day-neutral, permitting multiple crops to be grown per year. For example, flowers can be induced the year-round by introducing an OsMADSl transgene into floricultural species such as chrysanthemum and orchid. Delaying flowering and fruiting. By suppressing the expression of the OsMADSl gene by conventional approaches, e.g., by employing antisense, co- suppression, gene replacement, or other conventional approaches to suppressing plant gene expression, flowering and fruiting can be delayed. Delayed reproductive growth can thereby increase the length of the vegetative growth stage and cause the plants to grow faster, since the energy used for development of flowers and seeds can be saved for vegetative growth. Thus, delaying or eliminating reproductive growth results in a higher yield of vegetable species such as spinach, radish, cabbage, or tree species. In addition, such plants will be more desirable for as garden and street species, since their production of pollen allergens can be reduced or eliminated.

Overcoming the vernalization reouirement. The OsMADSl gene is useful for overriding the vernalization requirement of certain plant species. It is likely that the OsMADSl gene is the last (or almost last) gene expressed in the flower induction pathway. Therefore, induction of flowering of transgenic plants that constitutivelγ express the OsMADSl gene becomes insensitive to temperature.

Growing Plants in space. Plants grown extraterrestrially are preferably insensitive to photoperiod and temperature for flowering. Transgenic plants carrying the OsMADSl gene would be expected to flower in the extremely abnormal growth conditions found in a space shuttle or space station. Cloning and analysis of homoloαs of the OsMADSl oene in other plants.

The availability of the OsMADSl gene and its sequence makes it possible to obtain homologs of the OsMADSl gene in other organisms by conventional methods, through the use of nucleic acid and antibody probes and DNA primers based on the OsMADSl sequence, as described in greater detail below. These probes and primers are also useful in research on the patterns of expression and structure-function relationships for rice OsMADSl and its homologs, and for determining the interaction of these genes with other plant genes involved in floral development, for example. DEFINITIONS AND METHODS

The following definitions and methods are provided to better define the present invention and to guide those of ordinary skill in the art in the practice of the present invention. Definitions of common terms in molecular biology may also be found in Rieger et al.. Glossary of Genetics: Classical and Molecular, 5th edition, Springer- erlag: New York, 1991 ; and Lewin, Genes V, Oxford University Press: New York, 1994. The term "plant" encompasses any plant and progeny thereof. The term also encompasses parts of plants, including seed, cuttings, tubers, fruit, flowers, etc.

A "reproductive unit" of a plant is any totipotent part or tissue of the plant from which one can obtain a progeny of the plant, including, for example, seeds, cuttings, buds, bulbs, somatic embryos, etc. "Natural photoperiod conditions" are photoperiod (i.e., daylength) conditions as provided by sunlight at a given location, whether under field conditions. A photoperiod provided by artificial lighting but having a daylength approximating that of sunlight would also be considered a natural photoperiod condition. Nucleic Acids

Nucleic acids useful in the practice of the present invention comprise the isolated rice OsMADSl gene, its homologs in other plant species, and fragments and variants thereof. The term "OsMADSl " gene refers to a plant gene that contains a

MADS-box sequence, and preferably also a K-box sequence, and that is associated with one or more of the following phenotypes when expressed as a transgene in transgenic plants: (1 ) diminished apical dominance (as shown, for example, by dwarf stature); (2) early flowering; (3) altered daylength requirement for flowering; (4) greater synchronization of flowering; and (5) relaxed vernalization requirement. This term relates primarily to an isolated OsMADSl coding sequence, it also encompasses sequences comprising genomic sequences flanking the OsMADSl coding sequence that are operablγ linked to the coding sequence, including regulatory elements and/or intron sequences. Although the term "OsMADSl gene" most properly applies to the rice OsMADSl gene as shown in Fig. 1A, it is also intended to encompass alleles of the rice OsMADSl gene and homologs thereof from other plant species, such as the NtMADSI gene of Nicotiana tabacυm, as shown in Fig. 10. The term "OsMADSl gene" also encompasses "variant" forms of the gene (as detailed below) that have substantial homology to an OsMADSl sequence and OsMADSl biological activity. The term "native" refers to a naturally-occurring nucleic acid or polypeptide, including a wild-type sequence and an allele thereof.

A "homolog" of the OsMADSl gene is a native OsMADSl gene sequence isolated from a plant species other than Oriza sativa. The homolog has at least one of the biologically activities of OsMADSl , e.g., affecting apical dominance in transgenic plants, etc., as discussed above.

The nucleic acids of the present invention can be free in solution or attached by conventional means to a solid support, such as a hybridization membrane (e.g., nitrocellulose or nylon), a bead, or other solid supports known in the art.

"Isolated". An "isolated" nucleic acid has been substantially separated or purified away from other nucleic acid sequences in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA. The term "isolated" thus encompasses nucleic acids purified by standard nucleic acid-purification methods. The term also embraces nucleic acids prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids. DNA constructs incorporating an OsMADSl gene or fragment thereof according to the present invention preferably place the OsMADSl protein coding sequence under the control of an operablγ linked promoter that is capable of expression in a plant cell. Various promoters suitable for expression of heterologous genes in plant cells are known in the art, including constitutive promoters, e.g. the cauliflower mosaic virus (CaMV) 35S promoter, which is expressed in many plant tissues, organ- or tissue-specific promoters, and promoters that are inducible by chemicals such as methyl jasminate, salicylic acid, or Safener, for example. Plant transformation and regeneration. In addition to the methods for plant transformation and regeneration described in the Examples below for making transgenic plants, other well-known methods can be employed.

Fragments, probes, and primers. A fragment of an OsMADSl nucleic acid according to the present invention is a portion of the nucleic acid that is less than full-length and comprises at least a minimum length capable of hybridizing specifically with an OsMADSl nucleic acid according to the present invention (or a sequence complementary thereto) under stringent conditions as defined below. The length of such a fragment is preferably 15 nucleotides or more, although a shorter nucleic acid can be employed as a probe or primer if it is shown to specifically hybridize under stringent conditions with a target nucleic acid by methods well known in the art.

Nucleic acid probes and primers can be prepared based on nucleic acids according to the present invention, e.g., the OsMADSl gene of Fig. 1 A or the NtMADS3 gene of Fig. 10. A "probe" comprises an isolated nucleic acid attached to a detectable label or reporter molecule well known in the art. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes.

"Primers" are short nucleic acids, preferably DNA oligonucleotides 15 nucleotides or more in length, which are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a poiymerase, preferably a DNA poiymerase. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the poiymerase chain reaction (PCR) or other nucleic-acid amplification methods well known in the art. PCR-primer pairs can be derived from the sequence of a nucleic acid according to the present invention, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, ^e 1991 , Whitehead Institute for Biomedical Research, Cambridge, MA).

Methods for preparing and using probes and primers are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, ed. Sambrook et al.. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989; Current Protocols in Molecular Biology, ed. Ausubel et al., Greene Publishing and Wiley-lnterscience, New York, 1987 (with periodic updates); and Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press: San Diego, 1990. Probes or primers can be free in solution or covalently or noncovalently attached to a solid support by standard means.

Substantial similarity. A first nucleic acid is "substantially similar" to a second nucleic acid if, when optimally aligned (with appropriate nucleotide insertions or deletions) with the other nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 75%-90% of the nucleotide bases, and preferably greater than 90% of the nucleotide bases. ("Substantial sequence complementarity" requires a similar degree of sequence complementarity.) Sequence similarity can be determined by comparing the nucleotide sequences of two nucleic acids using sequence analysis software such as the Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, Madison, Wl.

Alternatively, two nucleic acids are substantially similar if they hybridize under stringent conditions, as defined below. Qperablv linked. A first nucleic-acid sequence is "operably" linked with a second nucleic-acid sequence when the first nucleic-acid sequence is placed in a functional relationship with the second nucleic-acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in reading frame.

"Recombinant". A "recombinant" nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an aαificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.

Techniques for nucleic-acid manipulation are described generally in, for example, Sambrook et al. (1989) and Ausubel et al. (1987, with periodic updates). Preparation of recombinant or chemically synthesized nucleic acids: vectors, transformation, host cells. Large amounts of a nucleic acid according to the present invention can be produced by recombinant means well known in the art or by chemical synthesis.

Natural or synthetic nucleic acids according to the present invention can be incorporated into recombinant nucleic-acid constructs, typically DNA constructs, capable of introduction into and replication in a host cell. Usually the DNA constructs will be suitable for replication in a unicellular host, such as E. coli or other commonly used bacteria, but can also be introduced into yeast, mammalian, plant or other eukaryotic cells.

Preferably, such a nucleic-acid construct is a vector comprising a replication system recognized by the host. For the practice of the present invention, well-known compositions and techniques for preparing and using vectors, host cells, introduction of vectors into host cells, etc. are employed, as discussed, inter alia, in Sambrook et al., 1989, or Ausubel et al., 1987.

A cell, tissue, organ, or organism into which has been introduced a foreign nucleic acid, such as a recombinant vector, is considered "transformed" or "transgenic." The DNA construct comprising an OsMADSl DNA sequence according to the present invention that is present in a transgenic host cell, particularly a transgenic plant, is referred to as a "transgene." The term "transgenic" or "transformed" when referring to a cell or organism, also includes (1 ) progeny of the cell or organism and (2) plants produced from a breeding program employing such a "transgenic" plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of the recombinant OsMADSl DNA construct.

Methods for chemical synthesis of nucleic acids are discussed, for example, in Beaucage and Carruthers, Tetra. Letts. 22:1859-1862, 1981 , and Matteucci et al., J. Am. Chem. Soc. 103:3185, 1981 . Chemical synthesis of nucleic acids can be performed, for example, on commercial automated oligonucleotide synthesizers.

Nucleic-Acid Hybridization: "Stringent Conditions": "Specific". The nucleic-acid probes and primers of the present invention hybridize under stringent conditions to a target DNA sequence, e.g., to the rice OsMADSl gene and its homologs in other plant species.

The term "stringent conditions" is functionally defined with regard to the hybridization of a nucleic-acid probe to a target nucleic acid (i.e., to a particular nucleic-acid sequence of interest) by the hybridization procedure discussed in Sambrook et al., 1989 at 9.52-9.55. See also, Sambrook et al., 1989 at 9.47-9.52, 9.56-9.58; Kanehisa, Nuc. Acids Res. 12:203-213, 1984; and Wetmur and Davidson, J. Mol. Biol. 31 :349-370, 1968.

Regarding the amplification of a target nucleic- acid sequence (e.g., by PCR) using a particular amplification primer pair, stringent conditions are conditions that permit the primer pair to hybridize only to the target nucleic-acid sequence to which a primer having the corresponding wild-type sequence (or its complement) would bind.

Nucleic-acid hybridization is affected by such conditions as salt concentration, temperature, or organic solvents, in addition to the base composition, length of the complementary strands, and the number of nucleotide- base mismatches between the hybridizing nucleic acids, as will be readily appreciated by those skilled in the art.

When referring to a probe or primer, the term "specific for (a target sequence)" indicates that the probe or primer hybridizes under stringent conditions only to the target sequence in a given sample comprising the target sequence.

Nucleic-acid amplification. As used herein, "amplified DNA" refers to the product of nucleic-acid amplification of a target nucleic-acid sequence. Nucleic-acid amplification can be accomplished by any of the various nucleic-acid amplification methods known in the art, including the poiymerase chain reaction (PCR). A variety of amplification methods are known in the art and are described, inter alia, in U.S. Patent Nos. 4,683,195 and 4,683,202 and in PCR Protocols: A Guide to Methods and Applications. Innis et al. eds., Academic Press, San Diego, 1990.

In situ hybridization. A number of techniques have been developed in which nucleic-acid probes are used to locate specific DNA sequences on intact chromosomes in situ, a procedure called "in situ hybridization." See, e.g., Pinkel et al., Proc. Natl. Acad. Sci. USA 85:9138-9142, 1988 (regarding fluorescence in situ hybridization), and Lengauer et al., Hum. Mol. Genet. 2:505-512, 1993 (regarding "chromosomal bar codes"). Well-known methods for in situ hybridization and for the preparation of probes or primers for such methods are employed in the practice of the present invention, including direct and indirect in situ hybridization methods.

Methods of making cDNA clones encoding OsMADSl or homoloos thereof. Based upon the availability of the OsMADSl and NtMADS3 cD As and the nucleotide sequences thereof, as disclosed herein, other OsMADSl genes (e.g., alleles and homologs of OsMADSl and NtMADS3) can be readily obtained from a wide variety of plants by cloning methods known in the art.

For example, one or more primer pairs based on the OsMADSl sequence can be used to amplify such OsMADSl genes or their homologs by the poiymerase chain reaction (PCR). Alternatively, the disclosed OsMADSl cDNA or fragments thereof can be used to probe a cDNA or genomic library made from a given plant species.

Cloning of the OsMADSl Genomic Gene and Homoloos Thereof. The availability of the OsMADSl cDNA sequence enables those skilled in the art to obtain a genomic clone corresponding to the OsMADSl cDNA (including the promoter and other regulatory regions and intron sequences) and the determination of its nucleotide sequence by conventional methods. Such an OsMADSl genomic clone and sequences derived therefrom are useful, for example, for studies of the expression of the OsMADSl gene. Nucleotide-Seouence Variants of OsMADSl cDNA and Amino Acid Seouence Variants of OsMADSl Protein. Using the nucleotide and the amino-acid sequence of the OsMADSl protein disclosed herein, those skilled in the art can create DNA molecules and polypeptides that have minor variations in their nucleotide or amino acid sequence.

"Variant" DNA molecules are DNA molecules containing minor changes in the native OsMADSl sequence, i.e., changes in which one or more nucleotides of a native OsMADSl sequence is deleted, added, and/or substituted while substantially maintaining OsMADSl biological activity. Variant DNA molecules can be produced, for example, by standard DNA mutagenesis techniques or by chemically synthesizing the variant DNA molecule. Such variants do not change the reading frame of the protein-coding region of the nucleic acid and encode a protein having no or only minor changes in OsMADSl biological function. Preferably, the mutations made in the native OsMADSl sequence do not create complementary regions that could produce secondary mRNA structure (see, e.g., EP 75, 444 A).

Amino-acid substitutions are preferably substitutions of single amino-acid residues. DNA insertions are preferably of about 1 to 10 contiguous nucleotides and deletions are preferably of about 1 to 30 contiguous nucleotides. Insertions and deletions are preferably insertions or deletions from an end of the protein-coding or non-coding sequence and are preferably made in adjacent base pairs. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a final construct.

Preferably, variant nucleic acids according to the present invention are "silent" or "conservative" variants. "Silent" variants are variants of a native rice OsMADSl sequence or a homolog thereof in which there has been a substitution of one or more base pairs but no change in the amino-acid sequence of the polypeptide encoded by the sequence. "Conservative" variants are variants of the native rice OsMADSl sequence or a homolog thereof in which at least one codon in the protein- coding region of the gene has been changed, resulting in a conservative change in one or more amino acid residues of the polypeptide encoded by the nucleic-acid sequence, i.e., an amino acid substitution. A number of conservative amino acid substitutions are listed in Table 3. In addition, one or more codons encoding cysteine residues can be substituted for, resulting in a loss of a cysteine residue and affecting disulfide linkages in the OsMADSl polypeptide. TABLE 1

Original Residue Conservative Substitutions

Ala ser

Arg lys

Asn gin, his Asp glu

Cys ser

Gin asn

Glu asp

Gly pro His asn; gin lie leu, val

Leu ile; val

Lys arg; gin; glu

Met leu; ile Phe met; leu; tyr

Ser thr

Thr ser

Trp tyr

Tyr trp; phe Val ile; leu

Substantial changes in function are made by selecting substitutions that are less conservative than those in Table 1 , i.e., selecting residues that differ more significantly in their effect on maintaining: (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation; (b) the charge or hydrophobicity of the molecule at the target site; or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in protein properties are those in which: (a) a hydrophilic residue, e.g., serγl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., Iγsyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine. Polvpeptides

The term "OsMADSl protein (or polypeptide)" refers to a protein encoded by an OsMADSl gene, including alleles and homologs of OsMADSl , or by a variant of the OsMADSl gene, having OsMADSl biological activity. An OsMADSl polypeptide can be isolated from a natural source, produced by the expression of a recombinant OsMADSl nucleic acid, or be chemically synthesized. Techniques for chemical synthesis of polypeptides are described, for example, in Merrifield, J. Amer. Chem. Soc. 85:2149-2156, 1963.

Pol^ype^ptide sequence homoloov. Ordinarily, the polypeptides encompassed by the present invention are at least about 70% homologous to a native OsMADSl polypeptide, preferably at least about 80% homologous, and more preferably at least about 95% homologous. Such homology is considered to be "substantial homology," although more important than shared amino-acid sequence homology can be the common possession of characteristic structural features and the retention of characteristic biological activity. Polypeptide homology is typically analyzed using sequence analysis software such as the Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, Madison, Wl). Polypeptide sequence analysis software matches homologous sequences using measures of homology assigned to various substitutions, deletions, substitutions, and other modifications.

"Isolated." "Purified." "Homogeneous" Polypeptides. A polypeptide is "isolated" if it has been separated from the cellular components (nucleic acids, lipids, carbohydrates, and other polypeptides) that naturally accompany it. Such a polypeptide can also be referred to as "pure" or "homogeneous" or "substantially" pure or homogeneous. Thus, a polypeptide which is chemically synthesized or recombinant (i.e., the product of the expression of a recombinant nucleic acid, even if expressed in a homologous cell type) is considered to be isolated. A monomeric polypeptide is isolated when at least 60-90% by weight of a sample is composed of the polypeptide, preferably 95% or more, and more preferably more than 99%. Protein purity or homogeneity is indicated, for example, by polyacrylamide gel electrophoresis of a protein sample, followed by visualization of a single polypeptide band upon staining the polyacrylamide gel; high pressure liquid chromatography; or other methods known in the art.

Protein purification. The polypeptides of the present invention can be purified by any of the means known in the art. Various methods of protein purification are described, e.g., in Guide to Protein Purification, ed. Deutscher, Meth. Enzymol. 185, Academic Press, San Diego, 1990; and Scopes, Protein Purification: Principles and Practice, Springer Verlag, New York, 1982.

Variant forms of OsMADSl polypeptides: labeling. Encompassed by the claimed OsMADSl polypeptides are variant polypeptides in which there have been substitutions, deletions, insertions or other modifications of the native OsMADSl polypeptide. The variants substantially retain structural and/or biological characteristics and are preferably silent or conservative substitutions of one or a small number of contiguous amino acid residues.

The native OsMADSl polypeptide sequence can be modified by conventional methods, e.g., by acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, and labeling, whether accomplished by in vivo or in vitro enzymatic treatment of an OsMADSl polypeptide or by the synthesis of an OsMADSl polypeptide using modified amino acids.

There are a variety of conventional methods and reagents for labeling polypeptides and fragments thereof. Typical labels include radioactive isotopes, ligands or ligand receptors, fluorophores, chemiluminescent agents, and enzymes. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed, e.g., in Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1 -3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1989; and Current Protocols in Molecular Biology, ed. Ausubel et al., Greene Publishing and Wiley-lnterscience: New York, 1987 (with periodic updates). Polypeptide Fragments. The present invention also encompasses fragments of OsMADSl polypeptides that lack at least one residue of a native full- length OsMADSl polypeptide yet retain at least one of the biological activities characteristic of rice OsMADSl . For example, the fragment can cause early flowering or dwarf phenotypes when expressed as a transgene in a host plant or possession of a characteristic immunological determinant. As an additional example, an immunologically active fragment of an OsMADSl polypeptide is capable of raising OsMADSl -specific antibodies in a target immune system (e.g., murine or rabbit) or of competing with OsMADSl for binding to OsMADSl -specific antibodies, and is thus useful in immunoassays for the presence of OsMADSl polypeptides in a biological sample. Such immunologically active fragments typically have a minimum size of 7 to 17 amino acids.

Fusion polypeptides. The present invention also provides fusion polypeptides including, for example, heterologous fusion polypeptides, i.e., an OsMADSl polypeptide sequence or fragment thereof and a heterologous polypeptide sequence, e.g., a sequence from a different polypeptide. Such heterologous fusion polypeptides thus exhibit biological properties (such as ligand-binding, catalysis, secretion signals, antigenic determinants, etc.) derived from each of the fused sequences. Fusion partners include, for example, immunoglobulins, beta galactosidase, trpE, protein A, beta lactamase, alpha amylase, alcohol dehγdrogenase, yeast alpha mating factor, and various signal and leader sequences which, e.g., can direct the secretion of the polypeptide. Fusion polypeptides are typically made by the expression of recombinant nucleic acids or by chemical synthesis. Polvoeptide sequence determination. The sequence of a polypeptide of the present invention can be determined by various methods known in the art. In order to determine the sequence of a polypeptide, the polypeptide is typically fragmented, the fragments separated, and the sequence of each fragment determined. To obtain fragments of an OsMADSl polypeptide, the polypeptide can be digested with an enzyme such as trypsin, clostripain, or Staphylococcυs protease, or with chemical agents such as cyanogen bromide, o-iodosobenzoate, hydroxylamine or 2-nitro-5-thiocyanobenzoate. Peptide fragments can be separated, e.g., by reversed-phase high-performance liquid chromatography (HPLC) and analyzed by gas-phase sequencing.

Polypeptide coupling to a solid phase support. The polypeptides of the present invention can be free in solution or coupled to a solid-phase support, e.g., nitrocellulose, nylon, column packing materials (e.g., Sepharose beads), magnetic beads, or glass wool. Antibodies

The present invention also encompasses polyclonal and/or monoclonal antibodies capable of specifically binding to OsMADSl polypeptides and fragments thereof, produced by conventional methods. Such antibodies are raised against an OsMADSl polypeptide and are capable of distinguishing the OsMADSl polypeptide from other polypeptides.

An immunological response is usually assayed with an immunoassaγ. Normally such immunoassays involve some purification of a source of antigen, for example, produced by the same cells and in the same fashion as the antigen was produced. For the preparation and use of antibodies according to the present invention, including various immunoassay techniques and applications, see, e.g., Goding, Monoclonal Antibodies: Principles and Practice, 2d ed, Academic Press, New York, 1986; and Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1988. OsMADSl -specific antibodies are useful, for example in purifying OsMADSl polypeptides from a biological sample, such as a host cell expressing recombinant OsMADSl polypeptides; in cloning OsMADSl homologs from rice or other plant species from an expression library; as antibody probes for protein blots and immunoassays; etc.

Frequently, the polypeptides and antibodies will be labeled by joining, either covalently or noncovalently, a substance which provides for a detectable signal. A wide variety of labels and conjugation techniques are known. Suitable labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent agents, chemiluminescent agents, magnetic particles and the like. The invention will be better understood by reference to the following Examples, which are intended to merely illustrate the best mode now known for practicing the invention. The scope of the invention is not to be considered limited thereto, however. E MELES

EXAMPLE 1 : Isolation and Analysis of a MADS-Box Gene from Rice. OsMADSl

Bacterial Strains. Plant Materials, and Plant Transformation. Escherichia coli MC1000 (ara, leu, lac, gal, str) was used as the recipient for routine cloning experiments. Rice (Oryza sativa L. cv. M201) plants were grown in a growth chamber at 26°C with 10.5-hr day cycle. cDNA Library Construction and Molecular Characterization. A cDNA library was constructed using the ΛZapll vector (Stratagene, La Jolla, CA) and poly(A) + mRNA isolated from rice flowers. An adapter containing fcoRI and Not\ sites (Pharmacia LKB Biotechnology, Piscatawaγ, NJ) was used to ligate the vector and cDNA. The library was divided into 20 sublibraries and amplified in an E. coli host strain, XL-1 Blue [F'::Tn10 pro + B + , laclq, (lac Z)MI5/recAJ. endAI, gyrA96 (Nar), thi, hsdR17(rk , mk⁴), sup44, reLA1 , lac] (Stratagene, La Jolla, CA).

Plaque hybridization was performed with 10⁶ plaques that were lifted onto nitrocellulose membranes. The plasmid pBluescript containing the OsMADSl cDNA was rescued in vivo from the bacteriophage λ using fl helper phage, R408 (Stratagene, La Jolla, CA). Both strands of the cDNA inserts were sequenced by the dideoxγnucleotide chain-termination method using double-stranded DNA as a template (Sanger et al„ Proc. Natl. Acad. Sci. USA 74:5463-5467, 1977).

Southern and Northern Blot Analyses. Genomic DNA was prepared from two-week-old rice seedlings by the CTAB (cetyltrimethylammoπium bromide) method (Rogers and Bendich, Extraction of DNA from plant tissues, In: Gelvin and Schilperoort, eds., Plant Molecular Biology Manual, Kluwer Academic, Dordrecht, Belgium, 1988, pp. A6/1 -10). Four μg of DNA were digested with appropriate restriction enzymes, separated on a 0.7% agarose gel, blotted onto a nylon membrane, and hybridized with a

"P-labeled probe labeled by the random-priming method (Sambrook et al.. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989). Ten //g of total RNA isolated by the guanidium thiocyanate method were used for the northern analysis (id.). In situ Localization. Rice flowers were dehydrated with ethanol, fixed

(1.4% glutaraldehyde, 2% paraformaldehyde. 50 mM PIPES, pH 7.2), and embedded in paraffin. Eight-μm sections were attached to gelatin-coated glass slides and hybridized with ^3ES-labeled antisense RNA (Cox and Goldberg, Analysis of plant gene expression. In: Shaw, ed., Plant Molecular Biology: A Practical Approach, IRL Press, Oxford, 1988, pp. 1-34). The RNA probe was prepared by in vitro transcription using pBluescript carrying the OsMADSl cDNA clone as a template. The sections were coated with an X-ray emulsion film and exposed for four days. The samples were stained with 0.5% toluidine blue to visualize tissue sections. Photographs were taken with a bright-field microscope.

Results. A cDNA clone, OsMADSl , was isolated by screening a λ Zapll cDNA library prepared from immature rice flower mRNA using mixed probes of different MADS-box cDNA clones isolated from Arabidopsis (Ma et al., Genes Dev. 5:484-495, 1991 ; Yanofsky et al.. Nature 346:35-39, 1990), Brassica (Mandel et al.. Cell 71 :133-143, 1992), tobacco (Kempin et al., Plant Physiol. 103:1041 -1046, 1933), and tomato (Pnueli et al., Plant J. 1 :255-266, 1991 ).

DNA sequence analysis showed that the rice clone encodes a protein of 257 amino-acid residues (Fig. 1A). The deduced amino-acid sequence contains the conserved MADS-box domain between amino acids 2 and 57 (Fig. 1 B). A second domain present in MADS-box proteins, the "K-box," is located between residues 90 and 143. The OsMADSl clone appears to be nearly full length, since the estimated transcript length by northern hybridization analysis is similar to that of the cDNA clone. The conserved MADS-box region is located immediately after the start methionine codon in the rice gene, as has been observed in most MADS-box genes. Therefore it is unlikely that the rice clone encodes a truncated protein.

These observations indicate that OsMADSl is a member of the MADS-box gene family. Among characterized MADS-box proteins, the OsMADSl amino-acid sequence is most homologous to API (44.4% identity) and SQUA (42.6% identity). In addition, OsMADSl shows extensive similarity to the functionally anonymous Arabidopsis MADS-box genes AGL2 (56.2% identity) and AGL4 (55.4% identity).

To determine the number of MADS-box genes present in rice, Southern blot analysis was performed. Figs. 2A and 2B show Southern blots of rice DNA digested with fcoRI (E), Hind\\\ (H), or Pst (P), fractionated on a 0.7% agarose gel, and hybridized with a probe prepared from the entire OsMADSl cDNA (Fig. 2A) or an OsMADSl cDNA probe lacking the conserved MADS-box region (Fig. 2B). More than ten restriction fragments hybridized with the entire cDNA probe, whereas a single fragment was detected by a probe lacking the conserved MADS-box region. This result indicates that the rice genome contains a large number of genes encoding MADS-box proteins, similar to what is observed in other plant species (Angenent et al., Plant Cell 4:983-993, 1992; Ma, Genes Dev. 5:484-495, 1991 ; Pnueli et al.. Plant J. 1 :255-266, 1991 ; Schmidt et al., Plant Cell 5:729-737, 1993). Northern blot analyses were conducted to study the expression pattern of the OsMADSl gene in rice. Figs. 3A and 3B show the OsMADSl expression pattern in rice organs. Ten- g samples of total RNA isolated from leaf (L) and root (R) of two- week-old seedlings, and anther (A), carpel (C), and palea/lemma (P) of anthesis-stage flowers was hybridized with the OsMADSl probe lacking the MADS domain. Ethidium bromide staining of 25S and 18S rRNAs demonstrated equal amounts of RNA loading. Figs. 3A and 3B also show the temporal expression pattern during flower development. Twenty μ of total RNA was isolated from rice flowers at different developmental stages: young inflorescence (panicle size < 1 cm), young flowers (panicle size = 1 to 6 cm), flowers at the early vacuolated pollen stage, and flowers at the late vacuolated pollen stage. This RNA was used for detection of OsMADSl gene expression. RNA samples were hybridized with the probe lacking the conserved MADS-box region in order to avoid cross-hybridization with other MADS-box genes and thus to observe the specific expression pattern of the gene. OsMADSl transcripts were present in the palea, lemma, and carpel, but not in the anther or vegetative organs (Fig. 3A). The gene was active during the young inflorescence stage and expression continued into the early and late vacuolated pollen stages (Fig. 3B).

Figs. 4A-4C show the localization of the OsMADSl transcript in rice flowers and phenotypes of transgenic tobacco plants expressing OsMADSl by in situ hybridization experiments using longitudinal sections of young inflorescence, and cross sections of the upper and lower rice flower at the vacuolated pollen stage (anther, filament, flower primordia, lemma, ovary, palea, sheath, and sterile lemma). 8- m sections were hybridized with ³⁶S-labeled antisense RNA lacking the MADS-box domain. The sections were coated with an X-ray emulsion film and exposed for four days. The samples were stained with 0.5% toluidine blue to visualize tissue sections which show negative expression of the gene. A sense probe did not show any hybridization above the background level. These in situ experiments revealed that the OsMADSl transcript was uniformly present in young flower primordia during early flower development and later became localized in certain floral organs (Figs. 4A-4C). In young inflorescences, strong hybridization signals were detected in flower primordia but not in other tissues (Fig. 4A). In vacuolated pollen-stage flowers, OsMADSl mRNA was detected in the palea, lemma, and ovary. However, the hybridization signal was not uniform in these tissues. In particular, the tissues near the palea/lemma junction and the palea tissues covered by lemma exhibited little or no expression of the gene. No significant signal was observed in the anther, filament, or sterile lemma. These results indicate that the OsMADSl gene is preferentially expressed in certain floral tissues, as has been observed with most MADS-box genes. The expression pattern of the OsMADSl gene closely resembled that of API and SQUA (Juijser et al., EMBO J. 1 1 :1239-1249, 1992; Mandel et al.. Nature 360:273-277, 1992). Flower-specific expression is also common for other MADS-box genes (Angenant et al., Plant Cell 4:983-993, 1992; Jack et al., Cell 68:683-697, 1992; Kempin et al., Plant Physiol. 103:1041-1046, 1993; Ma et al.. Genes Dev. 5:484-495, 1991 ; Mandel et al., Nature 360:273-277, 1992; Pnueli et al., Plant J. 1 :255-266, 1991 ; Schmidt et al., Plant Cell 5:729-737, 1993; Sommer et al., EMBO J. 9:605-613, 1990; Tsuchimoto et al., Plant Cell 5:843-853, 1993).

Nine independent clones that contain the conserved MADS-box have been isolated.

EXAMPLE 2: Expression of OsMADSl in Transgenic Tobacco Plants Results in Early Flowering and Dwarf Phenotypes

Bacterial Strains. Plant Materials, and Plant Transformation.

Agrobacteriυm tυmefaciens LBA4404 (Hoekema et al., Nature 303: 179-181 , 1983), containing the Ach5 chromosomal background and a disarmed helper-Ti plasmid pAL4404, was used for transformation of tobacco plants (Nicotiana tabacυm L. cv. Petit Havana SR1 ) by the co-cultivation method (An et al., Binary Vectors, In: Gelvin and Schilperoort, eds.. Plant Molecular Biology Manual, Kluwer Academic, Dordrecht, Belgium, 1988, pp. A3/1 -19). Transgenic plants were maintained in a greenhouse. Results. Ectopic expression of floral homeotic genes alters floral organ identity in homologous (Kempin et al., Plant Physiol. 103:1041 -1046, 1993; Mizukami and Ma, Cell 71 :1 19-131 , 1992; Pnueli et al., Plant Cell 6:163-173, 1994; Tsuchimoto et al., Plant Cell 5:843-853, 1993) and heterologous systems (Mandel et al., Cell 71 :133-143, 1992). In order to characterize the functional role of OsMADSl , tobacco plants were used as a heterologous expression system. The cDNA clone encoding the entire OsMADSl coding region was placed under the control of cauliflower mosaic virus 35S promoter (Benfey and Chua, Science 250:959-966, 1990) and transcript 7 terminator using a binary vector pGA748, which is a derivative of pGA643 (An et al.. Binary Vectors, In: Gelvin and Schilperoort, eds., Plant Molecular Biology Manual, Kluwer Academic, Dordrecht, Belgium, 1988, pp. A3/1-19). The chimeric molecule (pGA1209) was transferred to tobacco (Nicotiana tabacυm cv. Petite Havana SR1 ) plants using the Agrobacteriυm-mβάiated Ti plasmid vector system (An et al., Binary Vectors, In: Gelvin and Schilperoort, eds., Plant Molecular Biology Manual, Kluwer Academic, Dordrecht, Belgium, 1988, pp. A3/1-19). Twenty independent transgenic plants were studied.

Most of the primary transgenic plants flowered much earlier than control plants that were transformed with the Ti plasmid vector alone. The transgenic plants were significantly shorter and contained several lateral branches (Figs. 4D-4E). These phenotypes were inherited to the next generation as a dominant Mendelian trait.

Northern-blot analysis was conducted on seven transgenic plants which displayed the early flowering phenotype (Fig. 5). Transcripts from a control plant (C) and seven different transgenic plants (1 -7) exhibiting the early flowering and dwarf phenotypes were sampled for preparation of total RNA from leaves and flowers. Twenty μo of total RNA was hybridized with

³²P-labeled probe prepared from the OsMADSl cDNA lacking the MADS domain. The results (Fig. 5) showed that all of the transgenic plants accumulated the OsMADSl transcripts in both vegetative and reproductive organs. Although there were significant differences in gene expression among the transgenic plants, the relative expression level was similar between the leaf and flower. Transgenic plant Ml, which displayed the most severe symptoms, accumulated the highest level of the transcript. Plants #4, #5, #6, with less severely altered phenotypes, expressed the gene at reduced levels, indicating that the level of OsMADSl RNA correlated with phenotype. However, progeny from the same parent displayed phenotypic variation. The basis of this variation was investigated with T 1 offspring of the transgenic plant #2 in which the transgene segregates as a single locus. OsMADSl homozygotes were much shorter (34.2 ± 0.8 cm) compared to heterozygotes (51.6 ± 1.4 cm), while the wild-type tobacco plants were 1 19.8 ± 2.2 cm. The homozygotes flowered two days earlier than the heterozygotes and eight days earlier than wild type plants. This result indicates that the variation was due to gene dosage.

Table 2 summarizes characteristics of four independently transformed plants from the T1 generation. Seeds were collected from selfed fruits of the primary transgenic plants (TO generation). The seeds were germinated in a peat pellet and grown for two weeks at 16 hr light/8 hr dark cycles under fluorescent lights. The resulting T1 plants were grown under greenhouse conditions. Ten to twenty plants were analyzed for each transgenic line. Standard errors are shown in parentheses. Progeny carrying the transgenes were identified by visually scoring T2 seedlings for kanamycin resistance. The kanamycin-sensitive segregants were used as controls (C). Days to flowering include the time from seed germination to the first anthesis. Height and internode length were measured when fruits were fully developed (90 days postgermination). The data in Table 2 show that transgenic plants flowered 7 to 10 days earlier than wild-type plants and their height and internode length appear to be significantly reduced. TABLE 2; Comparison of phenotypes of transgenic plants with non-transformed control

Transgenic Days to Height Internode Length Line (#) Flowering (cm) (cm)

1 53.0 (2.0) 61.2 (5.8) 5.7 (0.5)

2 54.2 (0.3) 47.6 (1.9) 4.6 (0.2)

3 53.0 (0.4) 64.3 (3.5) 5.8 (0.3)

4 50.6 (0.9) 40.2 (4.4) 3.5 (0.3)

C 61.0 (0.2) 119.8 (2.2) 9.0 (0.3)

EXAMPLE 3: Ectooic Expression of OsMADSl Overcomes Photoperiod Dependency of Lono-Dav and Short-Day Flowering Plants

Transgenic plants that constitutively express a rice MADS-box gene,

OsMADSl, flower earlier than untransformed controls, indicating that the OsMADSl gene is involved in controlling flowering time. Nicotiana sylvestris. a long-day flowering plant, and N. tabacυm cv.

Maryland Mammoth, a short-day flowering plant, were transformed with pGA1209, which contains a kanamγcin selectable marker and a chimeric fusion between the CaMV 35S promoter and OsMADSl -coding region by the Agrobacteriυm-medlated co- cultivation method (An et al., Binary vectors, In Gelven and Schilperoort, eds., Plant Molecular Biology Manual A3: 1-19, Kluwer Academic Publishers, Dordrecht, Belgium, 1988). Transgenic plants were regenerated on kanamγcin-containing culture medium. Transgenic plants were selfed and kanamycin-resistant T 1 offspring were used for the entire experiment. Plants were grown under either a short-day growth condition (10 hr light) or a long-day growth condition (16 hr light). Total RNA was isolated from leaves of transgenic plants by the guanidium thiocyanate method (Sambrook et al.. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989). Twenty μg of total RNA was electrophoresed on a 1.3% agarose gel, blotted onto a nylon membrane, and hybridized with a ³²P-labeled probe prepared by the random-priming method (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989).

Transgenic N. sylvestris flowered earlier than untransformed controls under the permissive flowering (long-day) conditions. Plants were short and branched with clustered flowers compared to the controls. These phenotypes are similar to day- neutral transgenic tobacco plants expressing the OsMADSl gene.

In order to confirm whether the phenotypes were stably inherited, five independently transformed transgenic plants were chosen for further studies. T1 offspring were selected on a kanamycin-containing medium and the seedlings were grown under the long-day or short-day conditions. Under the long-day condition, the transgenic plants flowered 7-1 1 days earlier than the controls which flowered in 106 days after seed germination, as shown in Fig. 6A. The data are summarized in Table

3.

TABLE 3 Ectooic expression of OsMADSl in Nicotiana

Transgenic Short Day Condition (lOh) Long Day Condition (16h) Plant Days to Days to Flowering Height (cm) Flowering Height (cm)

1 102 62 98 68

2 85 35 95 45

3 146 65 99 72

4 84 36 96 46

5 97 52 97 52 control - 106 85

The transgenic plants also showed short and branched phenotypes. When the transgenic plants were grown under the short-day (non-permissive) condition, they flowered within 85-146 days, whereas the untransformed control plants did not flower (Fig. 6B, Table 3). Transgenic line 2 and 4 flowered earlier under the short-day condition and the line 3 flowered under the long-day condition, while the line 1 and 5 flowered at approximately the same time.

In order to confirm whether the phenotypes observed resulted from the expression of the OsMADSl gene, RNA blot analysis was performed. Since a constitutive promoter was used for expression of the gene, it was expected that the transcript was present in all the plant parts, since the 35S promoter-driven OsMADSl transcript is almost equally expressed in both leaves and flowers. Total RNA was prepared from fully expanded leaves of five transgenic lines and the level of OsMADSl transcript in each line was measured using the OsMADSl cDNA probe (Fig. 7).

All the transgenic plants expressed the OsMADSl transcript. The amount of the transcript was in direct correlation with the degree of the phenotypes. Transgenic lines 2 and 4, which flowered earliest, expressed the highest level of the OsMADSl mRNA, whereas line 3, which flowered latest among the five transgenic lines, expressed the lowest level of the OsMADSl mRNA. Transgenic lines with intermediate phenotypes expressed intermediate levels of the transcript.

These results suggest that expression of the OsMADSl gene caused a change in the timing of flowering in a long-day flowering plant N. sylvestris. Under permissive long-day conditions, transgenic plants flowered earlier than controls. Under non-permissive short-day conditions, expression of the transgene overcame the day¬ length requirement for flowering. The degree of the phenotype correlated with the level of expression of the transgene, especially under short-day conditions. Interestingly, transgenic plants expressing a high level of the OsMADS transcript flowered earlier under short-day conditions than under long-day conditions, the latter being permissive flowering conditions for untransformed N. sylvestris.

Expression of the OsMADSl gene can also overcome the day-length requirement of a short-day flowering plant, N. tabacυm cv. Maryland Mammoth. Transgenic plants were obtained that expressed the OsMADSl chimeric molecule. As observed with the day-neutral or long-day plant, transformation of the OsMADSl chimeric gene into the short-day plant resulted in early flowering and bushy phenotypes under a short-day (permissive) condition.

Three independently transformed lines were further studied. T1 offspring were selected on kanamycin-containing medium and grown under a short-day (permissive) or a long-day (non-permissive) conditions. Under permissive conditions, T1 transgenic lines flowered 6-21 days earlier than untransformed controls, which flowered in 19 days (Fig. 8A, Table 4). The height of the transgenic plants was less than one-half that of the control plants. Under non-permissive conditions, transgenic plants flowered in 202-206 days, whereas the control did not flower (Fig. 8B, Table 4-).

RNA blot analysis showed that all three lines expressed the OsMADSl transcript (Fig. 9). Again, the degree of the phenotype correlated with the level of

OsMADSl transgene expression. Thus, expression of the OsMADSl gene also overcame the day-length requirement of a short-day plant.

TABLE 4 ; Ectooic expression of OsMADSl in Nicotiana tabacum cv. Maryland Mammoth Transgenic Short Day Condition ( lOh) Long Day Condition ( 16h) Plant Days to Days to

Flowering Height (cm) Flowering Height (cm)

1 98 61 202 102

2 103 65 206 105

3 98 63 203 104 control 119 143 - -

Ectopic expression of OsMADSl overcomes the day-length dependence of flowering. The effect was more evident when the gene was highly expressed. The fact that OsMADSl overcomes the day-length dependence of both short-day and long- day plants indicates that a common gene product controls the timing of flowering in both short-day and long-day plants. It is likely that, under natural conditions, expression of the OsMADSl gene is tightly controlled by environmental conditions and the flowering process is initiated by triggering OsMADSl gene expression.

EXAMPLE 4: Isolation and Analysis of a MADS-Box Gene from Nicotiana tabacum. NtMAPS3

A homolog of OsMADSl was isolated from a Nicotiana tabacυm cDNA library constructed using the ΛZapll vector (Stratagene, La Jolla, CA) and poly(A) + mRNA isolated from tobacco flowers as described above. Using the OsMADSl cDNA as a probe under moderately stringent hybridization conditions (60 °C) in an initial screen, several tobacco MADS-box genes were obtained.

In a secondary screen to identify a tobacco homolog of OsMADSl , the OsMADSl cD A was split into two parts between the MADS-box and K-box sequences and used to probe the tobacco MADS-box cDNAs. Only one of the cDNAs, NtMADS3, hybridized to both halves of the OsMADSl sequence, i.e., to the half containing the MADS-box sequence and the half containing the OsMADSl K-box sequence.

To further confirm the identity of NtMADS3 as a homolog of OsMADSl , all isolated tobacco MADS-box genes obtained in the primary screening of the tobacco flower library were placed under the control of the 35S promoter and transformed into N. tabacυm as described above. Only transgenic N. tabacυm expressing the NtMADS3 transgene exhibited early flowering and dwarf phenotypes.

The nucleotide sequence of the NtMADS3 cDNA was obtained and compared to OsMADSl . NtMADS3 is 945 bp long and contains an open reading frame of 242 amino acid residues (Fig. 10). The deduced NtMADSI polypeptide sequence showed 56% homology with that of OsMADSl , with 96.5% homology in the MADS-box and 77.3% homology in the K-box (Fig. 1 1 ).

All publications and published patent documents cited in this specification are incorporated herein by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

This invention has been detailed both by example and by direct . description. It should be apparent that one having ordinary skill in the relevant art would be able to surmise equivalents to the invention as described in the claims which follow but which would be within the spirit of the foregoing description. Those equivalents are to be included within the scope of this invention.

Claims

1. An isolated nucleic acid comprising at least 15 contiguous nucleic acids of a sequence selected from the group consisting of:

(a) a native OsMADSl gene; and (b) a variant OsMADSl gene that is substantially similar in sequence to a native OsMADSl gene and, when expressed in a transgenic plant, produces at least one phenotype in the transgenic plant selected from the group consisting of: (i) diminished apical dominance, (ii) early flowering, (iii) altered daylength requirement for flowering; (iv) greater synchronization of flowering; and (v) relaxed vernalization requirement.

2. The nucleic acid of claim 1 wherein the sequence is a native OsMADSl gene.

3. The nucleic acid of claim 2 wherein the sequence is a native OsMADSl gene from Oriza sativa or Nicotiana tabacυm.

4. The nucleic acid of claim 3 wherein the sequence is that shown in Fig. lA or Fig. 10.

5. The nucleic acid of claim 1 wherein the sequence is a variant

OsMADSl gene that comprises only silent or conservative substitutions to a native

OsMADSl gene sequence.

6. A vector comprising the nucleic acid of claim 1.

7. A host cell comprising the nucleic acid of claim 1 .

8. A transgenic plant comprising the nucleic acid of claim 1 .

9. A purified polypeptide encoded by the nucleic acid of claim 1 .

10. A method of using the host cell of claim 7, the method comprising the steps of: providing the host cell; and culturing the host cell under conditions suitable for expression of the DNA sequence to produce an OsMADSl polypeptide.

1 1. A method of producing an OsMADSl polypeptide, the method comprising the steps of: providing the host cell of claim 7; and culturing the host cell under conditions suitable for expression of the DNA sequence to produce the OsMADSl polypeptide.

12. A method of using a nucleic acid of claim 1 comprising the steps of: introducing the nucleic acid of claim 1 into a plant cell, thereby producing a transformed plant cell; and growing a plant having an altered phenotype from the transformed plant cell.

13. A nucleic acid comprising a fragment of an OsMADSl gene capable of hybridizing under stringent conditions to a native OsMADSl gene sequence.

14. The nucleic acid of claim 13 further comprising a detectable label.

15. A method of obtaining an allele or homolog of the OsMADSl gene from a plant species comprising the steps of: providing a nucleic acid of the plant species; contacting the nucleic acid of the plant species with a DNA molecule under conditions allowing hybridization of the nucleic acid of the plant species and the DNA molecule, thereby producing a hybridization product, wherein the DNA molecule comprises a sequence from the group consisting of (i) a native OsMADSl gene and (ii) a fragment of a native OsMADSl gene capable of hybridizing under stringent conditions with the native OsMADSl gene; and identifying the allele or homolog.

16. The method of claim 15 wherein the DNA molecule comprises a detectable label.

17. The method of claim 15 further comprising performing an amplification reaction, thereby producing an amplification product, and the step of identifying comprises observing the amplification product.

18. An allele or homolog of the OsMADSl gene produced by the method of claim 15.

19. A method of producing a plant having at least one altered phenotype selected from the group consisting of (i) diminished apical dominance, (ii) early flowering, (iii) altered daylength requirement for flowering, (iv) greater synchronization of flowering, and (v) relaxed vernalization requirement, the method comprising the steps of:

(a) introducing into a cell of the plant a nucleic acid of claim 1 , thereby producing a transformed cell;

(b) growing a plant having the altered phenotype from the transformed cell.

20. A plant of a long-day or short-day species having a substantially relaxed daylength requirement for flowering.

21. The plant of claim 20 having a completely relaxed daylength requirement for flowering.

22. A method of producing multiple crops of flowers or fruits in a year from the plant of claim 20, the method comprising the steps of:

(a) planting a reproductive unit of the plant;

(b) growing the planted reproductive unit under natural light conditions;

(c) harvesting flowers or fruits of the plant; and (d) repeating steps (a) through (c) at least once in the year.

23. A transgenic plant exhibiting a phenotype that is significantly different from nontransgenic control plants with respect to at least one phenotype selected from the group consisting of:

(a) early flowering;

(b) altered daylength requirement for flowering; (c) greater synchronization of flowering; and

(d) relaxed vernalization requirement.