WO2006076099A2

WO2006076099A2 - Nucleotide sequences and corresponding polypeptides conferring modulated plant size and biomass in plants

Info

Publication number: WO2006076099A2
Application number: PCT/US2005/044380
Authority: WO
Inventors: Kenneth Feldmann; Greg Nadzan
Original assignee: Ceres, Inc.
Priority date: 2004-12-08
Filing date: 2005-12-08
Publication date: 2006-07-20
Also published as: US7663027B2; WO2006076099A3; US20100119690A1; US20060195943A1

Abstract

The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of modulated plant size, vegetative growth, organ number, plant architecture and/or biomass in plants. The present invention further relates to the use of these nucleic acid molecules and polypeptides in making transgenic plants, plant cells, plant materials or seeds of a plant having plant size, vegetative growth, organ number, plant architecture and/or biomass that are altered with respect to wild type plants grown under similar conditions.

Description

NUCLEOTIDE SEQUENCES AND CORRESPONDING POLYPEPTIDES CONFERRING MODULATED PLANT SIZE AND

BIOMASS IN PLANTS

FIELD OF THE INVENTION

[0001] This non-provisional application claims priority under 35 U.S. C.

§ 119(e) on U.S. Provisional Application Nos. 60/635,115 and 60/635,140 filed on December 8, 2005, the entire contents of which are hereby incorporated by reference.

[0002] The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able to modulate plant size, vegetative growth, organ number, architecture and/or biomass in plants. The present invention further relates to using the nucleic acid molecules and polypeptides to make transgenic plants, plant cells, plant materials or seeds of a plant having modulated size, vegetative growth, organ number, architecture and/or biomass as compared to wild-type plants grown under similar conditions.

BACKGROUND OF THE INVENTION

[0003] Plants specifically improved for agriculture, horticulture, biomass conversion, and other industries (e.g. paper industry, plants as production factories for proteins or other compounds) can be obtained using molecular technologies. As an example, great agronomic value can result from modulating the size of a plant as a whole or of any of its organs or the number of any of its organs.

[0004] Similarly, modulation of the size and stature of an entire plant, or a particular portion of a plant, allows production of plants better suited for a particular industry. For example, reductions in the height of specific crops and tree species can be beneficial by allowing easier harvesting. Alternatively, increasing height, thickness or organ number may be beneficial by providing more biomass useful for processing into food, feed, fuels and/or chemicals (http://www.eere.energy.gov/biomass/publications.html). Other examples of

/ commercially desirable traits include increasing the length of the floral stems of cut flowers, increasing or altering leaf size and shape or enhancing the size of seeds and/or fruits. Changes in organ size, organ number and biomass also result in changes in the mass of constituent molecules such as secondary products and convert the plants into factories for these compounds.

[0005] Availability and maintenance of a reproducible stream of food and feed to feed people has been a high priority throughout the history of human civilization and lies at the origin of agriculture. Specialists and researchers in the fields of agronomy science, agriculture, crop science, horticulture, and forest science are even today constantly striving to find and produce plants with an increased growth potential to feed an increasing world population and to guarantee a supply of reproducible raw materials. The robust level of research in these fields of science indicates the level of importance leaders in every geographic environment and climate around the world place on providing sustainable sources of food, feed and energy for the population..

[0006] Manipulation of crop performance has been accomplished conventionally for centuries through plant breeding. The breeding process is, however, both time-consuming and labor-intensive. Furthermore, appropriate breeding programs must be specially designed for each relevant plant species.

[0007] On the other hand, great progress has been made in using molecular genetics approaches to manipulate plants to provide better crops. Through introduction and expression of recombinant nucleic acid molecules in plants, researchers are now poised to provide the community with plant species tailored to grow more efficiently and produce more product despite unique geographic and/or climatic environments. These new approaches have the additional advantage of not being limited to one plant species, but instead being applicable to multiple different plant species (1).

/ [0008] Despite this progress, today there continues to be a great need for generally applicable processes that improve forest or agricultural plant growth to suit particular needs depending on specific environmental conditions. To this end, the present invention is directed to advantageously manipulating plant size, organ number, plant architecture and/or biomass to maximize the benefits of various crops depending on the benefit sought and the particular environment in which the crop must grow, characterized by expression of recombinant DNA molecules in plants. These molecules may be from the plant itself, and simply expressed at a higher or lower level, or the molecules may be from different plant species.

SUMMARY OF THE INVENTION

[0009] The present invention, therefore, relates to isolated nucleic acid molecules and polypeptides and their use in making transgenic plants, plant cells, plant materials or seeds of plants having life cycles, particularly plant size, vegetative growth, organ number, plant architecture and/or biomass, that are altered with respect to wild-type plants grown under similar or identical conditions.

[0010] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

BRIEF DESCRIPTION OF THE FIGURES

[0011] Figure 1. Amino acid sequence alignment of homologues of Lead

12/67, SEQ ID NO. 4. Conserved regions are enclosed in a box. A consensus sequence is shown below the alignment. [0012] Figure 2. Amino acid sequence alignment of homologues of Lead 17,

SEQ ID NO. 10. Conserved regions are enclosed in a box. A consensus sequence is shown below the alignment.

[0013] Figure 3. Amino acid sequence alignment of homologues of Lead 50,

SEQ ID NO. 17. Conserved regions are enclosed in a box. A consensus sequence is shown below the alignment.

[0014] Figure 4. Amino acid sequence alignment of homologues of Lead 58,

SEQ ID NO. 22. Conserved regions are enclosed in a box. A consensus sequence is shown below the alignment.

[0015] Figure 5. Amino acid sequence alignment of homologues of Lead

13/64, SEQ ID NO. 27. Conserved regions are enclosed in a box. A consensus sequence is shown below the alignment.

DETAILED DESCRIPTION OF THE INVENTION 1. THE INVENTION

[0016] The invention of the present application may be described by, but not necessarily limited to, the following exemplary embodiments.

[0017] The present invention discloses novel isolated nucleic acid molecules, nucleic acid molecules that interfere with these nucleic acid molecules, nucleic acid molecules that hybridize to these nucleic acid molecules, and isolated nucleic acid molecules that encode the same protein due to the degeneracy of the DNA code. Additional embodiments of the present application further include the polypeptides encoded by the isolated nucleic acid molecules of the present invention.

[0018] More particularly, the nucleic acid molecules of the present invention comprise: (a) a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively, (b) a nucleotide sequence that is complementary to any one of the nucleotide sequences according to (a), (c) a nucleotide sequence according to any one of SEQ ID Nos. 1, 9, 16, 21, 26 and 3, (d) a nucleotide sequence that is in reverse order of any one of the nucleotide sequences according to (c) when read in the 5' to 3' direction, (e) a nucleotide sequence able to interfere with any one of the nucleotide sequences according to (a), (f) a nucleotide sequence able to form a hybridized nucleic acid duplex with the nucleic acid according to any one of paragraphs (a) - (e) at a temperature from about 40⁰C to about 48°C below a melting temperature of the hybridized nucleic acid duplex, and (g) a nucleotide sequence encoding any one of amino acid sequences of Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively.

[0019] Additional embodiments of the present invention include those polypeptide and nucleic acid molecule sequences disclosed in SEQ ID NOS: 1-30.

[0020] The present invention further embodies a vector comprising a first nucleic acid having a nucleotide sequence encoding a plant transcription and/or translation signal, and a second nucleic acid having a nucleotide sequence according to the isolated nucleic acid molecules of the present invention. More particularly, the first and second nucleic acids may be operably linked. Even more particularly, the second nucleic acid may be endogenous to a first organism, and any other nucleic acid in the vector may be endogenous to a second organism. Most particularly, the first and second organisms may be different species.

[0021] In a further embodiment of the present invention, a host cell may comprise an isolated nucleic acid molecule according to the present invention. More particularly, the isolated nucleic acid molecule of the present invention found in the host cell of the present invention may be endogenous to a first organism and may be flanked by nucleotide sequences endogenous to a second organism. Further, the first and second organisms may be different species. Even more particularly, the host cell of the present invention may comprise a vector according to the present invention, which itself comprises nucleic acid molecules according to those of the present invention.

[0022] In another embodiment of the present invention, the isolated polypeptides of the present invention may additionally comprise amino acid sequences that are at least 85% identical to any one of Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively .

[0023] Other embodiments of the present invention include methods of introducing an isolated nucleic acid of the present invention into a host cell. More particularly, an isolated nucleic acid molecule of the present invention may be contacted to a host cell under conditions allowing transport of the isolated nucleic acid into the host cell. Even more particularly, a vector as described in a previous embodiment of the present invention, may be introduced into a host cell by the same method.

[0024] Methods of detection are also available as embodiments of the present invention. Particularly, methods for detecting a nucleic acid molecule according to the present invention in a sample. More particularly, the isolated nucleic acid molecule according to the present invention may be contacted with a sample under conditions that permit a comparison of the nucleotide sequence of the isolated nucleic acid molecule with a nucleotide sequence of nucleic acid in the sample. The results of such an analysis may then be considered to determine whether the isolated nucleic acid molecule of the present invention is detectable and therefore present within the sample.

[0025] A further embodiment of the present invention comprises a plant, plant cell, plant material or seeds of plants comprising an isolated nucleic acid molecule and/or vector of the present invention. More particularly, the isolated nucleic acid molecule of the present invention may be exogenous to the plant, plant cell, plant material or seed of a plant.

[0026] A further embodiment of the present invention includes a plant regenerated from a plant cell or seed according to the present invention. More particularly, the plant, or plants derived from the plant, plant cell, plant material or seeds of a plant of the present invention preferably has increased size (in whole or in part), increased vegetative growth, increased organ number and/or increased biomass (sometimes hereinafter collectively referred to as increased biomass) as compared to a wild-type plant cultivated under identical conditions. Furthermore, the transgenic plant may comprise a first isolated nucleic acid molecule of the present invention, which encodes a protein involved in early flowering, and a second isolated nucleic acid molecule which encodes a promoter capable of driving expression in plants, wherein the increased biomass component and the promoter are operably linked. More preferably, the gene conferring increased biomass may be mis- expressed in the transgenic plant of the present invention, and the transgenic plant exhibits an increased biomass as compared to a progenitor plant devoid of the gene, when the transgenic plant and the progenitor plant are cultivated under identical environmental conditions. In another embodiment of the present invention increased biomass phenotype may be due to the inactivation of a particular sequence, using for example an interfering RNA.

[0027] A preferred embodiment consists of a plant, plant cell, plant material or seed of a plant according to the present invention which comprises an isolated nucleic acid molecule of the present invention, wherein the plant, or plants derived from the plant, plant cell, plant material or seed of a plant, has increased biomass as compared to a wild-type plant cultivated under identical conditions.

[0028] Another embodiment of the present invention includes methods of enhancing biomass in plants. More particularly, these methods comprise transforming a plant with an isolated nucleic acid molecule according to the present invention. Preferably, the method is a method of enhancing biomass in the transformed plant, whereby the plant is transformed with a nucleic acid molecule encoding the polypeptide of the present invention.

[0029] Polypeptides of the present invention include consensus sequences. The consensus sequences are those as shown in Figures 1-5. 2. DEFINITIONS

[0030] The following terms are utilized throughout this application:

[0031] Biomass: As used herein, "biomass" refers to useful biological material including a product of interest, which material is to be collected and is intended for further processing to isolate or concentrate the product of interest. "Biomass" may comprise the fruit or parts of it or seeds, leaves, or stems or roots where these are the parts of the plant that are of particular interest for the industrial purpose. "Biomass", as it refers to plant material, includes any structure or structures of a plant that contain or represent the product of interest.

[0032] Transformation: Examples of means by which this can be accomplished are described below and include Agrobacterium-mediated transformation (of dicots (9-10), of monocots (11-13), and biolistic methods (14)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a To for the primary transgenic plant and Ti for the first generation.

[0033] Functionally Comparable Proteins or Functional Homologs: This term describes those proteins that have at least one functional characteristic in common. Such characteristics include sequence similarity, biochemical activity, transcriptional pattern similarity and phenotypic activity. Typically, the functionally comparable proteins share some sequence similarity or at least one biochemical. Within this definition, analogs are considered to be functionally comparable. In addition, functionally comparable proteins generally share at least one biochemical and/or phenotypic activity. [0034] Functionally comparable proteins will give rise to the same characteristic to a similar, but not necessarily the same, degree. Typically, comparable proteins give the same characteristics where the quantitative measurement due to one of the comparables is at least 20% of the other; more typically, between 30 to 40%; even more typically, between 50-60%; even more typically between 70 to 80%; even more typically between 90 to 100% of the other.

[0035] Heterologous sequences: "Heterologous sequences" are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3' end termination sequences that do not originate in nature from the same gene as the coding sequence, are considered heterologous to said coding sequence. Elements operatively linked in nature and contiguous to each other are not heterologous to each other. On the other hand, these same elements remain operatively linked but become heterologous if other filler sequence is placed between them. Thus, the promoter and coding sequences of a corn gene expressing an amino acid transporter are not heterologous to each other, but the promoter and coding sequence of a corn gene operatively linked in a novel manner are heterologous.

[0036] Misexpression: The term "misexpression" refers to an increase or a decrease in the transcription of a coding region into a complementary RNA sequence as compared to the wild-type. This term also encompasses expression and/or translation of a gene or coding region or inhibition of such transcription and/or translation for a different time period as compared to the wild-type and/or from a non-natural location within the plant genome. [0037] Percentage of sequence identity: As used herein, the term "percent sequence identity" refers to the degree of identity between any given query sequence and a subject sequence. A query nucleic acid or amino acid sequence is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment).

[0038] ClustalW calculates the best match between a query and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a query sequence, a subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2; window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For multiple alignment of nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: GIy, Pro, Ser, Asn, Asp, GIn, GIu, Arg, and Lys; residue-specific gap penalties: on. The output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher site (searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at the European Bioinformatics Institute site on the World Wide Web (ebi.ac.uk/clustalw).

[0039] In case of the functional homolog searches, to ensure a subject sequence having the same function as the query sequence, the alignment has to be along at least 80% of the length of the query sequence so that the majority of the query sequence is covered by the subject sequence. To determine a percent identity between a query sequence and a subject sequence, ClustalW divides the number of identities in the best alignment by the number of residues compared (gap positions are excluded), and multiplies the result by 100. The output is the percent identity of the subject sequence with respect to the query sequence. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.

[0040] Regulatory Regions: The term "regulatory region" refers to nucleotide sequences that, when operably linked to a sequence, influence transcription initiation or translation initiation or transcription termination of said sequence and the rate of said processes, and/or stability and/or mobility of a transcription or translation product. As used herein, the term "operably linked" refers to positioning of a regulatory region and said sequence to enable said influence. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5' and 3' untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, and introns. Regulatory regions can be classified in two categories, promoters and other regulatory regions.

[0041] Stringency: "Stringency," as used herein is a function of nucleic acid molecule probe length, nucleic acid molecule probe composition (G + C content), salt concentration, organic solvent concentration and temperature of hybridization and/or wash conditions. Stringency is typically measured by the parameter T_m, which is the temperature at which 50% of the complementary nucleic acid molecules in the hybridization assay are hybridized, in terms of a temperature differential from T_n,. High stringency conditions are those providing a condition of T_n, - 5⁰C to T_m - 10°C. Medium or moderate stringency conditions are those providing T_m - 2O⁰C to T_m - 29°C. Low stringency conditions are those

providing a condition of T_m - 40⁰C to T_n, - 48°C. The relationship between hybridization

conditions and T_m (in ⁰C) is expressed in the mathematical equation:

T_m = 81.5 -16.6(logio[Na⁺]) + 0.41(%G+C) - (600/N) (I)

where N is the number of nucleotides of the nucleic acid molecule probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below, for T_n, of DNA-DNA hybrids, is useful for probes having lengths in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide):

T_m = 81.5+16.6 log {[Na⁺]/(l+0.7[Na⁺])}+ 0.41(%G+C)-500/L 0.63(%formamide)

(H)

where L represents the number of nucleotides in the probe in the hybrid (21). The T_n, of Equation II is affected by the nature of the hybrid: for DNA-RNA hybrids, T_n, is 10-15°C

higher than calculated; for RNA-RNA hybrids, T_n, is 20-25⁰C higher. Because the T_n,

decreases about I⁰C for each 1% decrease in homology when a long probe is used (22), stringency conditions can be adjusted to favor detection of identical genes or related family members.

[0042] Equation II is derived assuming the reaction is at equilibrium.

Therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and allowing sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by using a hybridization buffer that includes a hybridization accelerator such as dextran sulfate or another high volume polymer.

[0043] Stringency can be controlled during the hybridization reaction, or after hybridization has occurred, by altering the salt and temperature conditions of the wash solutions. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8°C below T_m> medium or moderate stringency is 26-29°C below T_m and low stringency is 45-48°C below T_m.

[0044] To: The term "T₀" refers to the whole plant, explant or callus tissue, inoculated with the transformation medium.

[0045] Ti: The term Ti refers to either the progeny of the To plant, in the case of whole-plant transformation, or the regenerated seedling in the case of explant or callous tissue transformation.

[0046] T₂: The term T₂ refers to the progeny of the Ti plant. T₂ progeny are the result of self-fertilization or cross-pollination of a Ti plant.

[0047] T₃: The term T₃ refers to second generation progeny of the plant that is the direct result of a transformation experiment. T₃ progeny are the result of self-fertilization or cross-pollination of a T₂ plant.

3. IMPORTANT CHARACTERISTICS OF THE POLYNUCEOTIDES AND POLYPEPTIDES OF THE INVENTION

[0048] The nucleic acid molecules and polypeptides of the present invention are of interest because when the nucleic acid molecules are mis-expressed (i.e., when expressed at a non-natural location or in an increased or decreased amount relative to wild- type) they produce plants that exhibit modulated biomass as compared to wild-type plants, as evidenced by the results of various experiments disclosed below. This trait can be used to exploit or maximize plant products. For example, the nucleic acid molecules and polypeptides of the present invention are used to increase the expression of genes that cause the plant to have modulated biomass.

[0049] Because the disclosed sequences and methods increase vegetative growth, the disclosed methods can be used to enhance biomass production. For example, plants that grow vegetatively have an increase biomass production, compared to a plant of the same species that is not genetically modified for substantial vegetative growth. Examples of increases in biomass production include increases of at least 10%, at least 20%, or even at least 50%, when compared to an amount of biomass production by a plant of the same species not growing vegetatively.

[0050] The life cycle of flowering plants in general can be divided into three growth phases: vegetative, inflorescence, and floral (late inflorescence phase). In the vegetative phase, the shoot apical meristem (SAM) generates leaves that later will ensure the resources necessary to produce fertile offspring. Upon receiving the appropriate environmental and developmental signals the plant switches to floral, or reproductive, growth and the SAM enters the inflorescence phase (I) and gives rise to an inflorescence with flower primordia. During this phase the fate of the SAM and the secondary shoots that arise in the axils of the leaves is determined by a set of meristem identity genes, some of which prevent and some of which promote the development of floral meristems. Once established, the plant enters the late inflorescence phase (12) where the floral organs are produced. If the appropriate environmental and developmental signals the plant switches to floral, or reproductive, growth are disrupted, the plant will not be able to enter reproductive growth, therefore maintaining vegetative growth. 4. THE GENES OF THE INVENTION

[0051] The polynucleotides of the present invention and the proteins expressed via translation of these polynucleotides are set forth in the Sequence Listing, specifically SEQ ID Nos. 1-30. The Sequence Listing consists of functionally comparable proteins. Polypeptides comprised of a sequence within and defined by one of the consensus sequences can be utilized for the purposes of the invention, namely to make transgenic plants with modulated biomass.

5. USE OF THE GENES TO MAKE TRANSGENIC PLANTS

[0052] To use the sequences of the present invention or a combination of them or parts and/or mutants and/or fusions and/or variants of them, recombinant DNA constructs are prepared that comprise the polynucleotide sequences of the invention inserted into a vector and that are suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (see, 16) and can be introduced into the plant species of interest by, for example, Agrobacteήum-mediated transformation, or by other means of transformation, for example, as disclosed below.

[0053] The vector backbone may be any of those typically used in the field such as plasmids, viruses, artificial chromosomes, BACs, YACs, PACs and vectors such as, for instance, bacteria-yeast shuttle vectors, lamda phage vectors, T-DNA fusion vectors and plasmid vectors (see, 17-24).

[0054] Typically, the construct comprises a vector containing a nucleic acid molecule of the present invention with any desired transcriptional and/or translational regulatory sequences such as, for example, promoters, UTRs, and 3' end termination sequences. Vectors may also include, for example, origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, and introns. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker may preferably encode a biocide resistance trait, particularly antibiotic resistance, such as resistance to, for example, kanamycin, bleomycin, or hygromycin, or herbicide resistance, such as resistance to, for example, glyphosate, chlorosulfuron or phosphinotricin.

[0055] It will be understood that more than one regulatory region may be present in a recombinant polynucleotide, e.g., introns, enhancers, upstream activation regions, transcription terminators, and inducible elements. Thus, more than one regulatory region can be operably linked to said sequence.

[0056] To "operably link" a promoter sequence to a sequence, the translation initiation site of the translational reading frame of said sequence is typically positioned between one and about fifty nucleotides downstream of the promoter. A promoter can, however, be positioned as much as about 5,000 nucleotides upstream of the translation initiation site, or about 2,000 nucleotides upstream of the transcription start site. A promoter typically comprises at least a core (basal) promoter. A promoter also may include at least one control element, such as an enhancer sequence, an upstream element or an upstream activation region (UAR). For example, a suitable enhancer is a cis-regulatory element (-212 to -154) from the upstream region of the octopine synthase (ocs) gene. Fromm et ah, The Plant Cell 1:977-984 (1989).

[0057] _A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a "TATA box" element that may be located between about 15 and about 35 nucleotides upstream from the site of transcription initiation. Basal promoters also may include a "CCAAT box" element (typically the sequence CCAAT) and/or a GGGCG sequence, which can be located between about 40 and about 200 nucleotides, typically about 60 to about 120 nucleotides, upstream from the transcription start site. [0058] The choice of promoters to be included depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and cell- or tissue-preferential expression. It is a routine matter for one of skill in the art to modulate the expression of a sequence by appropriately selecting and positioning promoters and other regulatory regions relative to said sequence.

[0059] Some suitable promoters initiate transcription only, or predominantly, in certain cell types. For example, a promoter that is active predominantly in a reproductive tissue (e.g., fruit, ovule, pollen, pistils, female gametophyte, egg cell, central cell, nucellus, suspensor, synergid cell, flowers, embryonic tissue, embryo sac, embryo, zygote, endosperm, integument, or seed coat) can be used. Thus, as used herein a cell type- or tissue-preferential promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other cell types or tissues as well. Methods for identifying and characterizing promoter regions in plant genomic DNA include, for example, those described in the following references: Jordano, et al., Plant Cell, 1:855-866 (1989); Bustos, et al, Plant Cell, 1:839-854 (1989); Green, et al, EMBO J. 1, 4035-4044 (1988); Meier, et al, Plant Cell, 3, 309-316 (1991); and Zhang, et al, Plant Physiology 110: 1069-1079 (1996).

[0060] Examples of various classes of promoters are described below. Some of the promoters indicated below are described in more detail in U.S. Patent Application Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869; 60/583,691; 60/619,181; 60/637,140; 10/950,321; 10/957,569; 11/058,689; 11/172,703; 11/208,308; and PCT/US05/23639. It will be appreciated that a promoter may meet criteria for one classification based on its activity in one plant species, and yet meet criteria for a different classification based on its activity in another plant species.

[0061] Other Regulatory Regions: A 5' untranslated region (UTR) can be included in nucleic acid constructs described herein. A 5' UTR is transcribed, but is not translated, and lies between the start site of the transcript and the translation initiation codon and may include the +1 nucleotide. A 3' UTR can be positioned between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA stability or attenuating translation. Examples of 3' UTRs include, but are not limited to, polyadenylation signals and transcription termination sequences, e.g., a nopaline synthase termination sequence.

[0062] Various promoters can be used to drive expression of the genes of the present invention. Nucleotide sequences of such promoters are set forth in SEQ ID NOs: 31- 109. Some of them can be broadly expressing promoters, others may be more tissue preferential.

[0063] A promoter can be said to be "broadly expressing" when it promotes transcription in many, but not necessarily all, plant tissues or plant cells. For example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the shoot, shoot tip (apex), and leaves, but weakly or not at all in tissues such as roots or stems. As another example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the stem, shoot, shoot tip (apex), and leaves, but can promote transcription weakly or not at all in tissues such as reproductive tissues of flowers and developing seeds. Non-limiting examples of broadly expressing promoters that can be included in the nucleic acid constructs provided herein include the p326 (SEQ ID NO:), YP0144 (SEQ ID NO:), YP0190 (SEQ ID NO:), pl3879 (SEQ ID NO:), YP0050 (SEQ ID NO:), p32449 (SEQ ID NO:), 21876 (SEQ ID NO:), YP0158 (SEQ ID NO:), YP0214 (SEQ ID NO:), YP0380 (SEQ ID NO:), PT0848 (SEQ ID NO:), and PTO633 (SEQ ID NO:). Additional examples include the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1' or 2' promoters derived from T-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, and ubiquitin promoters such as the maize ubiquitin-1 promoter. In some cases, the CaMV 35S promoter is excluded from the category of broadly expressing promoters.

[0064] Root-active promoters drive transcription in root tissue, e.g., root endodermis, root epidermis, or root vascular tissues. In some embodiments, root-active promoters are root-preferential promoters, i.e., drive transcription only or predominantly in root tissue. Root-preferential promoters include the YPO 128 (SEQ ID NO: 82), YP0275 (SEQ ID NO: 93), PT0625 (SEQ ID NO: 36), PT0660 (SEQ ID NO: 39), PT0683 (SEQ ID NO: 44), and PT0758 (SEQ ID NO: 52). Other root-preferential promoters include the PT0613 (SEQ ID NO: 35), PT0672 (SEQ ID NO: 41), PT0688 (SEQ ID NO: 45), and PT0837 (SEQ ID NO: 54), which drive transcription primarily in root tissue and to a lesser extent in ovules and/or seeds. Other examples of root-preferential promoters include the root-specific subdomains of the CaMV 35S promoter (Lam et al, Proc. Natl. Acad. Sci. USA 86:7890-7894 (1989)), root cell specific promoters reported by Conkling et al, Plant Physiol. 93:1203-1211 (1990), and the tobacco RD2 gene promoter.

[0065] hi some embodiments, promoters that drive transcription in maturing endosperm can be useful. Transcription from a maturing endosperm promoter typically begins after fertilization and occurs primarily in endosperm tissue during seed development and is typically highest during the cellularization phase. Most suitable are promoters that are active predominantly in maturing endosperm, although promoters that are also active in other tissues can sometimes be used. Non-limiting examples of maturing endosperm promoters that can be included in the nucleic acid constructs provided herein include the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter (Bustos et al., Plant Cell l(9):839-853 (1989)), the soybean trypsin inhibitor promoter (Riggs et al, Plant Cell l(6):609-621 (1989)), the ACP promoter (Baerson et al, Plant MoI Biol, 22(2):255-267 (1993)), the stearoyl-ACP desaturase gene (Slocombe et al, Plant Physiol 104(4): 167- 176 (1994)), the soybean α' subunit of β-conglycinin promoter (Chen et al, Proc Natl Acad Sci USA 83:8560-8564 (1986)), the oleosin promoter (Hong et al., Plant MoI Biol 34(3):549-555 (1997)), and zein promoters, such as the 15 kD zein promoter, the 16 kD zein promoter, 19 kD zein promoter, 22 kD zein promoter and 27 kD zein promoter. Also suitable are the Osgt- 1 promoter from the rice glutelin-1 gene (Zheng et al, MoI. Cell Biol. 13:5829-5842 (1993)), the beta-amylase gene promoter, and the barley hordein gene promoter. Other maturing endosperm promoters include the YP0092 (SEQ ID NO: 68), PT0676 (SEQ ID NO: 42), and PT0708 (SEQ ID NO: 47).

[0066] Promoters that drive transcription in ovary tissues such as the ovule wall and mesocarp can also be useful, e.g., a polygalacturonidase promoter, the banana TRX promoter, and the melon actin promoter. Other such promoters that drive gene expression preferentially in ovules are YP0007 (SEQ ID NO: 60), YPOlI l (SEQ ID NO: 76), YP0092 (SEQ ID NO: 68), YP0103 (SEQ ID NO: 73), YP0028 (SEQ ID NO: 63), YP0121 (SEQ ID NO: 81), YP0008 (SEQ ID NO: 61), YP0039 (SEQ ID NO: 64), YPOl 15 (SEQ ID NO: 77), YPOl 19 (SEQ ID NO: 62), YPO 120 (SEQ ID NO: 80)andYP0374 (SEQ ID NO: 98).

[0067] In some other embodiments of the present invention, embryo sac/early endosperm promoters can be used in order drive transcription of the sequence of interest in polar nuclei and/or the central cell, or in precursors to polar nuclei, but not in egg cells or precursors to egg cells. Most suitable are promoters that drive expression only or predominantly in polar nuclei or precursors thereto and/or the central cell. A pattern of transcription that extends from polar nuclei into early endosperm development can also be found with embryo sac/early endosperm-preferential promoters, although transcription typically decreases significantly in later endosperm development during and after the cellularization phase. Expression in the zygote or developing embryo typically is not present with embryo sac/early endosperm promoters. [0068] Promoters that may be suitable include those derived from the following genes: Arabidopsis viviparous-1 (see, GenBank No. U93215); Arabidopsis atmycl (see, Urao (1996) Plant MoI. Biol., 32:571-57; Conceicao (1994) Plant, 5:493-505); Arabidopsis FIE (GenBank No. AF 129516); Arabidopsis MEA; Arabidopsis FIS2 (GenBank No. AF096096); and FIE 1.1 (U.S. Patent 6,906,244). Other promoters that may be suitable include those derived from the following genes: maize MACl (see, Sheridan (1996) Genetics, 142:1009- 1020); maize Cat3 (see, GenBank No. L05934; Abler (1993) Plant MoI. Biol., 22:10131- 1038). Other promoters include the following Arabidopsis promoters: YP0039 (SEQ ID NO: 64), YPOlOl (SEQ ID NO: 71), YP0102 (SEQ ID NO: 72), YPOl 10 (SEQ ID NO: 75), YPOl 17 (SEQ ID NO: 78), YPOl 19 (SEQ ID NO: 79), YP0137 (SEQ ID NO: 83), DME, YP0285 (SEQ ID NO: 94), and YP0212 (SEQ ID NO: 90). Other promoters that may be useful include the following rice promoters: p530cl0, pOsFIE2-2, pOsMEA, pOsYpl02, and pOsYp285.

[0069] Promoters that preferentially drive transcription in zygotic cells following fertilization can provide embryo-preferential expression and may be useful for the present invention. Most suitable are promoters that preferentially drive transcription in early stage embryos prior to the heart stage, but expression in late stage and maturing embryos is also suitable. Embryo-preferential promoters include the barley lipid transfer protein (Ltpl) promoter (Plant Cell Rep (2001) 20:647-654, YP0097 (SEQ ID NO: 70), YP0107 (SEQ ID NO: 74), YP0088 (SEQ ID NO: 67), YP0143 (SEQ ID NO: 84), YP0156 (SEQ ID NO: 86), PT0650 (SEQ ID NO: 38), PT0695 (SEQ ID NO: 46), PT0723 (SEQ ID NO: 49), PT0838 (SEQ ID NO: 55), PT0879 (SEQ ID NO: 58) and PT0740 (SEQ ID NO: 50).

[0070] Promoters active in photosynthetic tissue in order to drive transcription in green tissues such as leaves and stems are of particular interest for the present invention. Most suitable are promoters that drive expression only or predominantly such tissues. Examples of such promoters include the ribulose-l,5-bisphosphate carboxylase (RbcS) promoters such as the RbcS promoter from eastern larch (Larix laricina), the pine cabό promoter (Yamamoto et al, Plant Cell Physiol. 35:773-778 (1994)), the Cab-1 gene promoter from wheat (Fejes et al., Plant MoI. Biol. 15:921-932 (1990)), the CAB-I promoter from spinach (Lubberstedt et al, Plant Physiol. 104:997-1006 (1994)), the cablR promoter from rice (Luan et al, Plant Cell 4:971-981 (1992)), the pyruvate orthophosphate dikinase (PPDK) promoter from corn (Matsuoka et al, Proc Natl Acad. Sci USA 90:9586-9590 (1993)), the tobacco Lhcbl*2 promoter (Cerdan et al, Plant MoI Biol 33:245-255 (1997)), the Arabidopsis thaliana SUC2 sucrose-H+ symporter promoter (Truernit et al, Planta 196:564- 570 (1995)), and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS. Other promoters that drive transcription in stems, leafs and green tissue are PT0535 (SEQ ID NO: 33), PT0668 (SEQ ID NO: 32), PT0886 (SEQ ID NO: 59), PR0924 (SEQ ID NO: 108), YP0144 (SEQ ID NO: 85), YP0380 (SEQ ID NO: 100) and PT0585 (SEQ ID NO: 34).

[0071] In some other embodiments of the present invention, inducible promoters may be desired. Inducible promoters drive transcription in response to external stimuli such as chemical agents or environmental stimuli. For example, inducible promoters can confer transcription in response to hormones such as giberellic acid or ethylene, or in response to light or drought. Examples of drought inedible promoters are YP0380 (SEQ ID NO: 100), PT0848 (SEQ ID NO: 56), YP0381 (SEQ ID NO: 101), YP0337 (SEQ ID NO: 96), YP0337 (SEQ ID NO: 96), PT0633 (SEQ ID NO: 37), YP0374 (SEQ ID NO: 98), PT0710 (SEQ ID NO: 48), YP0356 (SEQ ID NO: 97), YP0385 (SEQ ID NO: 103), YP0396 (SEQ ID NO: 104), YP0384 (SEQ ID NO: 102), YP0384 (SEQ ID NO: 102), PT0688 (SEQ ID NO: 45), YP0286 (SEQ ID NO: 95), YP0377 (SEQ ID NO: 99), and PD1367 (SEQ ID NO: 109). Examples of promoters induced by nitrogen are PT0863 (SEQ ID NO: 57), PT0829 (SEQ ID NO: 53), PT0665 (SEQ ID NO: 40) and PT0886 (SEQ ID NO: 59). An example of a shade inducible promoter is PR0924.

[0072] Other Promoters: Other classes of promoters include, but are not limited to, leaf-preferential, stem/shoot-preferential, callus-preferential, guard cell-preferential, such as PT0678 (SEQ ID NO: 43), and senescence-preferential promoters. Promoters designated YP0086 (SEQ ID NO: 66), YPOl 88 (SEQ ID NO: 88), YP0263 (SEQ ID NO: 92), PT0758 (SEQ ID NO: 52), PT0743 (SEQ ID NO: 51), PT0829 (SEQ ID NO: 53), YPOl 19 (SEQ ID NO: 79), and YP0096 (SEQ ID NO: 69), as described in the above-referenced patent applications, may also be useful.

[0073] Alternatively, misexpression can be accomplished using a two component system, whereby the first component consists of a transgenic plant comprising a transcriptional activator operatively linked to a promoter and the second component consists of a transgenic plant that comprise a nucleic acid molecule of the invention operatively linked to the target- binding sequence/region of the transcriptional activator. The two transgenic plants are crossed and the nucleic acid molecule of the invention is expressed in the progeny of the plant. In another alternative embodiment of the present invention, the misexpression can be accomplished by having the sequences of the two component system transformed in one transgenic plant line.

[0074] Another alternative consists in inhibiting expression of a biomass- modulating polypeptide in a plant species of interest. The term "expression" refers to the process of converting genetic information encoded in a polynucleotide into RNA through transcription of the polynucleotide (i.e., via the enzymatic action of an RNA polymerase), and into protein, through translation of mRNA. "Up-regulation" or "activation" refers to regulation that increases the production of expression products relative to basal or native states, while "down-regulation" or "repression" refers to regulation that decreases production relative to basal or native states.

[0075] A number of nucleic-acid based methods, including anti-sense RNA, ribozyme directed RNA cleavage, and interfering RNA (RNAi) can be used to inhibit protein expression in plants. Antisense technology is one well-known method. In this method, a nucleic acid segment from the endogenous gene is cloned and operably linked to a promoter so that the antisense strand of RNA is transcribed. The recombinant vector is then transformed into plants, as described above, and the antisense strand of RNA is produced. The nucleic acid segment need not be the entire sequence of the endogenous gene to be repressed, but typically will be substantially identical to at least a portion of the endogenous gene to be repressed. Generally, higher homology can be used to compensate for the use of a shorter sequence. Typically, a sequence of at least 30 nucleotides is used (e.g., at least 40, 50, 80, 100, 200, 500 nucleotides or more).

[0076] Thus, for example, an isolated nucleic acid provided herein can be an antisense nucleic acid to one of the aforementioned nucleic acids encoding a biomass- modulating polypeptide. A nucleic acid that decreases the level of a transcription or translation product of a gene encoding a biomass-modulating polypeptide is transcribed into an antisense nucleic acid similar or identical to the sense coding sequence of the biomass- modulating polypeptide. Alternatively, the transcription product of an isolated nucleic acid can be similar or identical to the sense coding sequence of a biomass-modulating polypeptide, but is an RNA that is unpolyadenylated, lacks a 5' cap structure, or contains an unsplicable intron.

[0077] In another method, a nucleic acid can be transcribed into a ribozyme, or catalytic RNA, that affects expression of an mRNA. (See, U.S. Patent No. 6,423,885). Ribozymes can be designed to specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. Heterologous nucleic acids can encode ribozymes designed to cleave particular mRNA transcripts, thus preventing expression of a polypeptide. Hammerhead ribozymes are useful for destroying particular mRNAs, although various ribozymes that cleave mRNA at site-specific recognition sequences can be used. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target RNA contain a 5'-UG-3' nucleotide sequence. The construction and production of hammerhead ribozymes is known in the art. See, for example, U.S. Patent No. 5,254,678 and WO 02/46449 and references cited therein. Hammerhead ribozyme sequences can be embedded in a stable RNA such as a transfer RNA (tRNA) to increase cleavage efficiency in vivo. Perriman, et al., Proc. Natl. Acad. Sci. USA, 92(13):6175-6179 (1995); de Feyter and Gaudron, Methods in Molecular Biology, Vol. 74, Chapter 43, "Expressing Ribozymes in Plants", Edited by Turner, P.C, Humana Press Inc., Totowa, NJ. RNA endoribonucleases such as the one that occurs naturally in Tetrahymena thermophila, and which have been described extensively by Cech and collaborators can be useful. See, for example, U.S. Patent No. 4,987,071.

[0078] Methods based on RNA interference (RNAi) can be used. RNA interference is a cellular mechanism to regulate the expression of genes and the replication of viruses. This mechanism is thought to be mediated by double-stranded small interfering RNA molecules. A cell responds to such a double-stranded RNA by destroying endogenous mRNA having the same sequence as the double-stranded RNA. Methods for designing and preparing interfering RNAs are known to those of skill in the art; see, e.g., WO 99/32619 and WO 01/75164. For example, a construct can be prepared that includes a sequence that is transcribed into an interfering RNA. Such an RNA can be one that can anneal to itself, e.g., a double stranded RNA having a stem-loop structure. One strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sense coding sequence of the polypeptide of interest, and that is from about 10 nucleotides to about 2,500 nucleotides in length. The length of the sequence that is similar or identical to the sense coding sequence can be from 10 nucleotides to 500 nucleotides, from 15 nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides, or from 25 nucleotides to 100 nucleotides. The other strand of the stem portion of a double stranded RNA comprises an antisense sequence of the biomass-modulating polypeptide of interest, and can have a length that is shorter, the same as, or longer than the corresponding length of the sense sequence. The loop portion of a double stranded RNA can be from 10 nucleotides to 5,000 nucleotides, e.g., from 15 nucleotides to 1,000 nucleotides, from 20 nucleotides to 500 nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portion of the RNA can include an intron. See, e.g., WO 99/53050.

[0079] In some nucleic-acid based methods for inhibition of gene expression in plants, a suitable nucleic acid can be a nucleic acid analog. Nucleic acid analogs can be modified at the base moiety, sugar moiety, or phosphate backbone to improve, for example, stability, hybridization, or solubility of the nucleic acid. Modifications at the base moiety include deoxyuridine for deoxythymidine, and 5-methyl-2'-deoxycytidine and 5-bromo-2'- deoxycytidine for deoxycytidine. Modifications of the sugar moiety include modification of the T hydroxyl of the ribose sugar to form 2'-O-methyl or 2'-O-allyl sugars. The deoxyribose phosphate backbone can be modified to produce morpholino nucleic acids, in which each base moiety is linked to a six-membered morpholino ring, or peptide nucleic acids, in which the deoxyphosphate backbone is replaced by a pseudopeptide backbone and the four bases are retained. See, for example, Summerton and Weller, 1997, Antisense Nucleic Acid Drug Dev., 7:187-195; Hyrup et al, 1996, Bioorgan. Med. Chem., 4: 5-23. In addition, the deoxyphosphate backbone can be replaced with, for example, a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite, or an alkyl phosphotriester backbone.

Transformation

[0080] Nucleic acid molecules of the present invention may be introduced into the genome or the cell of the appropriate host plant by a variety of techniques. These techniques, able to transform a wide variety of higher plant species, are well known and described in the technical and scientific literature {see, e.g., 28-29).

[0081] A variety of techniques known in the art are available for the introduction of DNA into a plant host cell. These techniques include transformation of plant cells by injection (30), microinjection (31), electroporation of DNA (32), PEG (33), use of biolistics (34), fusion of cells or protoplasts (35), and via T-DNA using Agrobacterium tumefaciens (36-37) or Agrobacterium rhizogenes (38) or other bacterial hosts (39), for example.

[0082] In addition, a number of non-stable transformation methods that are well known to those skilled in the art may be desirable for the present invention. Such methods include, but are not limited to, transient expression (40) and viral transfection (41).

[0083] Seeds are obtained from the transformed plants and used for testing stability and inheritance. Generally, two or more generations are cultivated to ensure that the phenotypic feature is stably maintained and transmitted.

[0084] A person of ordinary skill in the art recognizes that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. [0085] The nucleic acid molecules of the present invention may be used to confer the trait of an altered flowering time.

[0086] The nucleic acid molecules of the present invention encode appropriate proteins from any organism, but are preferably found in plants, fungi, bacteria or animals.

[0087] The methods according to the present invention can be applied to any plant, preferably higher plants, pertaining to the classes of Angiospermae and Gymnospermae. Plants of the subclasses of the Dicotylodenae and the Monocotyledonae are particularly suitable. Dicotyledonous plants belonging to the orders of the Magniolales, Middles, Laurales, Piperales Aristochiales, Nymphaeales, Ranunculales, Papeverales, Sarraceniaceae, Trochodendrales, Hamamelidales, Eucomiales, Leitneriales, Myricales, Fagales, Casuarinales, Caryophyllales, Batales, Polygonales, Plumbaginales, Dilleniales, Theales, Malvales, Urticales, Lecythidales, Violates, Salicales, Capparales, Ericales, Diapensales, Ebenales, Primulales, Resales, Fabales, Podostemales, Haloragales, Myrtales, Cornales, Proteales, Santales, Rafflesiales, Celastrales, Euphorbiales, Rhamnales, Sapindales, Juglandales, Geraniales, Polygalales, Umbellales, Gentianales, Polemoniales, Lamiales, Plantaginales, Scrophulariales, Campanulales, Rubiales, Dipsacales, and Asterales, for example, are also suitable. Monocotyledonous plants belonging to the orders of the Alismatales, Hydrocharitales, Najadales, Triuridales, Commelinales, Eriocaulales, Restionales, Poales, Juncales, Cyperales, Typhales, Bromeliales, Zingiberales, Arecales, Cyclanthales, Pandanales, Arales, Lilliales, and Orchidales also may be useful in embodiments of the present invention. Further examples include, but are not limited to, plants belonging to the class of the Gymnospermae are Pinales, Ginkgoales, Cycadales and Gnetales.

[0088] The methods of the present invention are preferably used in plants that are important or interesting for agriculture, horticulture, biomass for bioconversion and/or forestry. Non-limiting examples include, for instance, tobacco, oilseed rape, sugar beet, potatoes, tomatoes, cucumbers, peppers, beans, peas, citrus fruits, avocados, peaches, apples, pears, berries, plumbs, melons, eggplants, cotton, soybean, sunflowers, roses, poinsettia, petunia, guayule, cabbages, spinach, alfalfa, artichokes, sugarcane, mimosa, Serviced lespedera, corn, wheat, rice, rye, barley, sorghum and grasses such as switch grass, giant reed, Bermuda grass, Johnson grass or turf grass, millet, hemp, bananas, poplars, eucalyptus trees and conifers.

Homologues Encompassed by the Invention

[0089] It is known in the art that one or more amino acids in a sequence can be substituted with other amino acid(s), the charge and polarity of which are similar to that of the substituted amino acid, i.e. a conservative amino acid substitution, resulting in a biologically/functionally silent change. Conservative substitutes for an amino acid within the polypeptide sequence can be selected from other members of the class to which the amino acid belongs. Amino acids can be divided into the following four groups: (1) acidic (negatively charged) amino acids, such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids, such as arginine, histidine, and lysine; (3) neutral polar amino acids, such as serine, threonine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as glycine, alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, cysteine, and methionine.

[0090] Nucleic acid molecules of the present invention can comprise sequences that differ from those encoding a protein or fragment thereof selected from the group consisting of [leads 11, 17, 50, 58, 64, and 67, nucleotides] due to the fact that the different nucleic acid sequence encodes a protein having one or more conservative amino acid changes. [0091] Biologically functional equivalents of the polypeptides, or fragments thereof, of the present invention can have about 10 or fewer conservative amino acid changes, more preferably about 7 or fewer conservative amino acid changes, and most preferably about 5 or fewer conservative amino acid changes. In a preferred embodiment of the present invention, the polypeptide has between about 5 and about 500 conservative changes, more preferably between about 10 and about 300 conservative changes, even more preferably between about 25 and about 150 conservative changes, and most preferably between about 5 and about 25 conservative changes or between 1 and about 5 conservative changes.

Identification of Useful Nucleic Acid Molecules and Their Corresponding Nucleotide Sequences

[0092] The nucleic acid molecules, and nucleotide sequences thereof, of the present invention were identified by use of a variety of screens that are predictive of nucleotide sequences that provide plants with altered size, vegetative growth, organ number, plant architecture and/or biomass. One or more of the following screens were, therefore, utilized to identify the nucleotide (and amino acid) sequences of the present invention.

[0093] The present invention is further exemplified by the following examples.

The examples are not intended to in any way limit the scope of the present application and its uses.

6. EXPERIMENTS CONFIRMING THE USEFULNESS OF THE

POLYNUCLEOTIDES AND POLYPEPTIDES OF THE INVENTION General Protocols Agrobacterium-Mediated Transformation of Λrabidopsis [0094] Wild-type Arabidopsis thaliana Wassilewskija (WS) plants are transformed with Ti plasmids containing clones in the sense orientation relative to the 35 S promoter. A Ti plasmid vector useful for these constructs, CRS 338, contains the Ceres- constructed, plant selectable marker gene phosphinothricin acetyltransferase (PAT), which confers herbicide resistance to transformed plants.

[0095] Ten independently transformed events are typically selected and evaluated for their qualitative phenotype in the Ti generation.

[0096] Preparation of Soil Mixture: 24L SunshineMix #5 soil (Sun Gro

Horticulture, Ltd., Bellevue, WA) is mixed with 16L Therm-O-Rock vermiculite (Therm-O- Rock West, Inc., Chandler, AZ) in a cement mixer to make a 60:40 soil mixture. To the soil mixture is added 2 Tbsp Marathon 1% granules (Hummert, Earth City, MO), 3 Tbsp OSMOCOTE^® 14-14-14 (Hummert, Earth City, MO) and 1 Tbsp Peters fertilizer 20-20-20 (J.R. Peters, Inc., Allentown, PA), which are first added to 3 gallons of water and then added to the soil and mixed thoroughly. Generally, 4-inch diameter pots are filled with soil mixture. Pots are then covered with 8-inch squares of nylon netting.

[0097] Planting: Using a 60 mL syringe, 35 mL of the seed mixture is aspirated. 25 drops are added to each pot. Clear propagation domes are placed on top of the pots that are then placed under 55% shade cloth and subirrigated by adding 1 inch of water.

[0098] Plant Maintenance: 3 to 4 days after planting, lids and shade cloth are removed. Plants are watered as needed. After 7-10 days, pots are thinned to 20 plants per pot using forceps. After 2 weeks, all plants are subirrigated with Peters fertilizer at a rate of 1 Tsp per gallon of water. When bolts are about 5-10 cm long, they are clipped between the first node and the base of stem to induce secondary bolts. Dipping infiltration is performed 6 to 7 days after clipping. [0099] Preparation of Agrobacterium: To 150 mL fresh YEB is added 0.1 mL each of carbenicillin, spectinomycin and rifampicin (each at 100 mg/ml stock concentration). Agrobacterium starter blocks are obtained (96-well block with Agrobacterium cultures grown to an ODδoo of approximately 1.0) and inoculated one culture vessel per construct by transferring 1 mL from appropriate well in the starter block. Cultures are then incubated with shaking at 27°C. Cultures are spun down after attaining an ODgoo of approximately 1.0 (about 24 hours). 200 mL infiltration media is added to resuspend Agrobacterium pellets. Infiltration media is prepared by adding 2.2 g MS salts, 50 g sucrose, and 5 μl 2 mg/ml benzylaminopurine to 900 ml water.

[00100] Dipping Infiltration: The pots are inverted and submerged for 5 minutes so that the aerial portion of the plants are in the Agrobacterium suspension. Plants are allowed to grow normally and seed is collected.

[00101] High-throughput Phenotypic Screening of Misexpression Mutants:

Seed is evenly dispersed into water-saturated soil in pots and placed into a dark 4°C cooler for two nights to promote uniform germination. Pots are then removed from the cooler and covered with 55% shade cloth for 4-5 days. Cotyledons are fully expanded at this stage. FINALE^® (Sanofi Aventis, Paris, France) is sprayed on plants (3 ml FINALE^® diluted into 48 oz. water)and repeated every 3-4 days until only transformants remain.

[00102] Screening: Screening is routinely performed at four stages: Seedling,

Rosette, Flowering, and Senescence. o Seedling - the time after the cotyledons have emerged, but before the 3^rd true leaf begins to form. o Rosette - the time from the emergence of the 3 ^r true leaf through just before the primary bolt begins to elongate. o Flowering - the time from the emergence of the primary bolt to the onset of senescence (with the exception of noting the flowering time itself, most observations should be made at the stage where approximately 50% of the flowers have opened). o Senescence - the time following the onset of senescence (with the exception of "delayed senescence", most observations should be made after the plant has completely dried). Seeds are then collected.

[00103] Screens: Screening for increased size, vegetative growth and/or biomass is performed by taking measurements, specifically T₂ measurements were taken as follows:

• Days to Bolt = number of days between sowing of seed and emergence of first inflorescence.

• Rosette Leaf Number at Bolt = number of rosette leaves present at time of emergence of first inflorescence.

• Rosette Area = area of rosette at time of initial inflorescence emergence, using formula ((LxW)*3.14)/4.

• Height = length of longest inflorescence from base to apex. This measurement was taken at the termination of flowering/onset of senescence.

• Primary Inflorescence Thickness = diameter of primary inflorescence 2.5 cm up from base. This measurement was taken at the termination of flowering/onset of senescence.

• Inflorescence Number = total number of unique inflorescences. This measurement was taken at the termination of flowering/onset of senescence. [00104] PCR was used to amplify the cDNA insert in one randomly chosen T₂ plant.

This PCR product was then sequenced to confirm the sequence in the plants.

7. RESULTS

Example 1: Lead ll;(ME01795; Ceres cDNA 5662747; clone 8161)

[00105] Ten independently transformed events were selected and evaluated for their qualitative phenotype in the T₁ generation as per standard protocol. Three events showing the strongest T₁ phenotypes were chosen for evaluation in the T₂ generation. The T₂ growth conditions followed the above Ti protocol. The experimental design differed from the Ti planting in that each T₂ plant was contained with its own pot, and no herbicide selection was used. All the pots for each T₂ event were contained within the same flat and the plants were randomly distributed within each flat. The controls for each set of measurements were the segregating progeny of other Ti events which did not contain this gene (internal controls). All analyses were done via soil-based experiments under long day light conditions (16 hours) in the Ceres greenhouse.

[00106] All ten events showed a variety of phenotypes different from wild-type transgenic controls (Table 1. The most pronounced variant phenotype was that of reduced secondary inflorescence formation, slightly delayed flowering time, larger rosettes with more leaves, and tall, thick inflorescences.

Table 1. Qualitative phenotypes observed in 35S::cDNA 5662747 Ti events

[00107] Events 01, 04, and 10 were evaluated in greater detail in the T₂ generation. Fourteen individuals were sown for each event. The transgenic plants of all 3 events showed increased height, primary inflorescence thickness, and delay of flowering time to a 0.01 level of statistical significance (Table 2). These plants also had qualitatively larger rosettes which contained more leaves (data not shown). All plants, noted in the table as MEO 1795-01, MEO 1795-04, or MEO 1795- 10, were segregating progeny of the Ti event which we had confirmed to contain the transgene under test. All plants noted in the table as - 01 Control, -04 Control, or -10 Controls were segregating progeny of the Ti event which did not contain the transgene under test (internal controls).

[00108] One item of note in the T₂ analysis is that the reduced secondary inflorescence formation observed in Ti plants is no longer present in T₂ plants. In addition, the delay in flowering time appears to have increased in severity from the Ti to T₂ generation.

[00109] Segregation frequencies of the transgene under test suggest that each event contains a single insert, as determined by a Chi-square test (data not shown).

Table 2. Quantitative phenotypes seen in 35S::cDNA 5662747 T₂ events

[00110] Summary of results:

• Hie ectopic expression of cDNA 5662747 with a strong constitutive promoter (35S) results in taller plants, with thicker inflorescences, a larger rosette, and more rosette leaves.

• 5662747 is normally expressed in shoot and root apices, suggesting that the encoded protein may help to regulate meristem function.

• The increase in plant size seen by this expression is accompanied by a delay in flowering time, but no reduction in fertility.

• As the Ti plants had a much less severe delay in flowering than the T₂ plants, but still produced the large-plant phenotype, it may be possible to use a promoter of different strength or with a different spatial expression pattern with the cDNA to maintain an increase in plant height and stem/inflorescence thickness without any increase in flowering time.

• It may also be a useful gene to increase root growth, given the similar expression pattern in shoot meristems and root tip cells. [00111] As a result, this gene is useful to increase vegetative biomass to give an improved source:sink ratio and improved fixation of carbon to sucrose and starch. Taller inflorescences give the opportunity for more flowers and therefore more seeds. The combination of improved biomass and inflorescence stature can give a significant improvement in yield. Thicker inflorescences can prevent against "snap" against wind, rain or drought and there was no detectable difference in fertility factors such as silique number and seed fill.

Example 2: Lead 12/67; ME03459 and ME04358; Ceres cDNA 12337825/ 14296577; Clone 8490/96

[00112] Experiments were performed substantially as described in Example 1, but with different seeds. Ten independently transformed events were selected and evaluated for their qualitative phenotype in the Ti generation as per standard protocol. Two events showing the most advantageous Ti phenotypes (large, late-flowering) were chosen for evaluation in the T₂ generation. The T₂ growth conditions follow the above Ti protocol. The experimental design differs from the Ti planting in that each T₂ plant is contained within its own pot, and no herbicide selection is used. All pots for each T₂ event are contained within the same flat and the plants are randomly distributed within each flat. The controls for each set of measurements are the segregating progeny of the given Ti event which do not contain the T-DNA (internal controls). All analyses are done via soil-based experiments under long day light conditions (16 hours) in the Ceres greenhouse.

[00113] All ten events were late flowering, produced larger rosettes with more leaves and tall, thick inflorescences compared to the controls (Table 3). The transgenic "control" was a set of different 35S cDNA expressing plants which were indistinguishable from the untransformed WS wild type. Table 3. Qualitative phenotypes observed in 35S::cDNA 12337825 Ti events

[00114] Events ME03459-01 and ME03459-04 were evaluated in greater detail in the T₂ generation. Seventeen individuals were sown and observed for event 01, whereas 18 individuals were sown and observed for event 04. The transgenic plants for both events showed increased height, increased primary inflorescence thickness, increased number of rosette leaves, a larger rosette, and delay of flowering time to a 0.05 level of statistical significance (Table 4). Both events had normal fertility. All plants noted in the table as ME03459-01 or ME03459-04 were segregating progeny of the Ti event which we had confirmed to contain the transgene under test. All plants noted in the table as -01 Control or - 04 Control were segregating progeny of the given Tl event, which did not contain the transgene (internal controls). [00115] Both events produce significantly more seeds than the control, as would be expected for a typical, fertile, late flowering plant.

[00116] Event ME03459-01 exhibited the strongest as noted in Table 4. The rosette area, number of leaves, thickness of the inflorescence and days to bolt are all greater than event -04.

[00117] Segregation frequencies of the transgene under test suggest that each event contains a single insert, as calculated by a Chi-square test.

Table 4. Quantitative phenotypes observed in 35S::cDNA 12337825 T₂ events

[00118] Summary of Results:

• The ectopic expression of cDNA 12337825 with a strong constitutive promoter (35S) results in taller plants, with thicker inflorescences, a larger rosette, and increased number of rosette leaves.

• 12337825 is normally regulated in shoot and root apices, suggesting that the encoded protein may help to regulate meristem function.

• The increase in plant size observed by this expression is accompanied by a delay in flowering time, but no reduction in fertility. • It is also a useful gene to increase root growth, given the similar expression pattern in shoot meristems and root tip cells.

[00119] As a result, this gene is useful to increase vegetative biomass and give an improved source:sink ratio and improved fixation of carbon to sucrose and starch, and to improved yield. Taller inflorescences give the opportunity for more flowers and therefore more seeds. The combination of improved biomass and inflorescence stature can give a significant improvement in yield. In addition, thicker inflorescences can prevent "snap" against wind, rain or drought.

[00120] ME04358 was identified from a Ti screen looking for mutant developmental and morphological phenotypes. All four independent transgenic events containing Clone 96 (ME04358) were screened in the Ti generation for the presence of mutant developmental and morphological phenotypes. All events were taller with larger rosettes than wildtype.

[00121] Events ME04358-01 and -02 show 3:1 and 15:1 (R:S) segregation for Finale™, respectively. Event ME04358-01 showed a Mendelian segregation of 3:1 (R:S) for Finale™ in the T₂ generation. Event ME04358-02 segregated 15:1 (R:S) for Finale™ in the T₂ generation.

[00122] Both T₂ events of ME04358 show increased rosette/leaf size and inflorescence height compared to controls. Events ME04358-01 and -02 were tested for the quantitative traits of Plant Size. When grown under constant light, both events had significantly larger rosettes and taller inflorescences with a p-value less than or equal to 0.05 (Table 5). Both events were also slightly, yet statistically significantly later flowering than controls. Both events trended toward having slightly thicker inflorescences than the controls, but these data were not statistically significant at p<0.05. Under long-day conditions, the plants were larger than controls but had an exaggerated delay in flowering time. Table 5. Analysis of Rosette Area, Primary Inflorescence Thickness, Plant Height, and Days to Flowering for ME04358-01 & -02. Both events had statistically larger rosettes, taller inflorescences, and a slight delay in flowering. All values denote the mean of the population.

[00123] Summary of Results:

[00124] The four Ti plants were larger and taller than the controls. Events

ME04358-01 and -02 were screened.

• Germination - No detectable reduction in germination rate

• General morphology/architecture - Plants were larger than the controls

• Days to flowering - A statistical delay in flowering was observed for both events

• Rosette area 7 days post-bolting - The rosettes of both events were larger than controls

• Plant height - An increase in height was observed for both events

• Fertility (silique number and seed fill) - No observable differences between experimentals and controls. Example 3: Lead 13/64; ME01990; Ceres cDNA 12420510/1434106; clone 258241/25821

[00125] Four independently transformed events were selected and evaluated for their qualitative phenotype in the Ti generation as per standard protocol. Two events showing the most advantageous Tj phenotypes (large plants with larger rosettes, more leaves and tall, thick inflorescences) were chosen for evaluation in the T₂ generation. The T₂ growth conditions follow the above Ti protocol. The experimental design differs from the Ti planting in that each T₂ plant is contained within its own pot, and no herbicide selection is used. All pots for each T₂ event are contained within the same flat and the plants are randomly distributed within each flat. The controls for each set of measurements are the segregating progeny of the given Ti event which do not contain the T-DNA (internal controls). All analyses are done via soil-based experiments under long day light conditions (16 hours) in the Ceres greenhouse.

[00126] Two of the 4 events produced larger rosettes with more leaves and tall, thick inflorescences (Table 6) compared to the controls. The transgenic "control" was a set of different 35S::cDNA expressing plants which were indistinguishable from the untransformed WS wildtype.

Table 6. Qualitative phenotypes observed in 35S::cDNA 12420510 Ti events

[00127] Events MEO 1990-02 and MEO 1990-03 were evaluated in greater detail in the T₂ generation. Eighteen individuals were sown and observed for each event. The transgenic plants for both events showed increased height, increased number of rosette leaves, a larger rosette, and delay of flowering time to a 0.05 level of statistical significance (Table 7). Although both events had visibly thicker inflorescences in the Tl generation, only event -03- proved to be quantitatively thicker to a 0.05 level of statistical significance (Table 7). Both events had normal fertility. All plants noted in the table as MEO 1990-02 and MEO 1990-03 were segregating progeny of the Ti event which we had confirmed to contain the transgene under test. All plants noted in the table as -02 Control or -03 Control were segregating progeny of given Tl events which did not contain the transgene (internal controls).

[00128] Both events produce significantly more seeds than the control, as would be expected for a typical, fertile, late flowering plant.

[00129] Event MEO 1991-02 had 6 transgene-containing plants which exhibited the beneficial phenotype and 8 transgene-containing plants which appeared wild-type (not included in the statistical analysis in Table 7). Event MEO 1991-03 had 7 transgene- containing plants which exhibited the beneficial phenotype and 1 transgene-containing plant which appeared wild-type. Our statistical analyses compared the internal controls to those plants with the beneficial phenotype which contained the transgene.

[00130] Segregation frequencies of the transgene under test suggest that each event contains a single insert, as calculated by a Chi-square test.

[00131] Summary of results:

• The ectopic expression of cDNA 12420510 with a strong constitutive promoter (35S) results in taller plants, a larger rosette, and more rosette leaves.

• The increase in plant size seen by this expression is accompanied by a slight delay in flowering time, but no reduction in fertility. This would be a particularly useful gene to employ in crop plants because flowering time is only slightly delayed.

[00132] As a result, this gene is useful to increase vegetative biomass and give an improved sourcersink ratio and improved fixation of carbon to sucrose and starch, and to improved yield. Taller inflorescences give the opportunity for more flowers and therefore more seeds. The combination of improved biomass and inflorescence stature can give a significant improvement in yield. In addition, thicker inflorescences can prevent "snap" against wind, rain or drought.

ME01990-01, -03; Ceres cDNA 14301106; clone 25821

[00133] T₂ plants were scored quantitatively for the previously observed Plant Size phenotype and statistical significance was determined, as per protocol, with one exception. Twelve segregating experimentals and 12 external controls were sown per flat per event.

[00134] ME01990 was identified from a Ti screen looking for mutant developmental and morphological phenotypes. All 4 independent transgenic events containing Clone 258241 (MEO 1990) were screened in the Ti generation for the presence of mutant developmental and morphological phenotypes. Events -02 and -03 appeared larger than the rest of the population.

[00135] Both events of MEO 1990 show 3 : 1 segregation for Finale™.

[00136] Both T₂ events of MEO 1990 show increased rosette/leaf size and inflorescence thickness compared to controls. MEO 1593, containing the same construct yielded similar results. Events ME01990-02 and -03 were tested for the quantitative traits of Plant Size. Both events had significantly larger rosettes and thicker inflorescences with a p- value less than or equal to 0.05 (Table 8). Event -03 was also slightly, yet statistically significantly later flowering than controls. However, the degree of flowering delay falls within the window of acceptable flowering time as negative phenotypes are defined. Both events trended toward being slightly taller than the controls, but these data were not statistically significant at p<0.05. When the two events of MEOl 990 were grown in constant light, they were wildtype in appearance.

[00137] hi an unrelated experiment, events of ME01593 (also 35S::258241) were tested for the noted quantitative plant size traits under long day conditions. The results of this experiment were equivalent to those of MEO 1990. MEO 1593 events had larger rosettes, thicker inflorescences, and were delayed in time to flowering.

[00138] From the Ti analyses of the degree of biomass and late flowering, 14 of the large late flowering lines were tested in the T₂ generation under long day and constant light conditions. Most of the 14 lines were severely delayed in flowering under long day and constant light conditions, but several, while delayed in flowering under long day conditions, exhibited a wildtype phenotype under constant light. As such, MEO 1990 is a late flowering line that has an increased biomass but less than four days delay in flowering under long day conditions. Table 8. Analysis of Rosette Area, Primary Inflorescence Thickness, Plant Height, and Day to Flowering for ME01990-02 & -03. Both events had statistically larger rosettes and thicker inflorescences. All values denote the mean of the population.

[00139] Events -02 and -03 of MEO 1990 were screened. Twelve segregating transformants from each event were screened instead of 18, and 12 external wild-type controls were screened instead of 6.

[00140] Summary of results:

• Germination - no detectable reduction in germination rate

• General morphology/architecture -plants were larger than the controls

• Days to flowering - A statistical delay in flowering was observed for Event -03 but not for -02.

• Plant height - No observable differences between experimentals and controls

• Fertility (silique number and seed fill) - No observable differences between experimentals and controls. Example 4: Lead 17; ME04249; Ceres cDNA 13495746; clone 37288

[00141] Ten independently transformed events were selected and evaluated for their qualitative phenotype in the Ti generation as per standard protocol. Two events showing the most advantageous Ti phenotypes (plants with larger rosettes, more leaves and thick inflorescences) were chosen for evaluation in the T₂ generation. The T₂ growth conditions follow the above Ti protocol. The experimental design differs from the Ti planting in that each T₂ plant is contained within its own pot, and no herbicide selection is used. All pots for each T₂ event are contained within the same flat and the plants are randomly distributed within each flat. The controls for each set of measurements are the segregating progeny of the given Ti event which do not contain the T-DNA (internal controls). All analyses are done via soil-based experiments under long day light conditions (16 hours) in the Ceres.

[00142] Five of the 10 events produced larger rosettes with more leaves and thicker inflorescences compared to the controls. These plants were also delayed in flowering time but exhibited normal fertility. Four other events were smaller and/or had fertility defects (Table 9). The transgenic "control" was a set of plants expressing a different 35S::cDNA and which were indistinguishable from the untransformed WS wildtype.

[00143] Events ME04249-03 and ME04249-07 were evaluated in greater detail in the T₂ generation. Eighteen individuals were sown and observed for each event. The transgenic plants showed increased primary inflorescence thickness, increased number of rosette leaves, a larger rosette, and delay of flowering time to a 0.05 level of statistical significance (Table 10). ME04249-07 was also significantly taller than the controls. All plants noted in Table 10 were segregating progeny of the T₁ event which had been confirmed to contain the transgene under test. However, all plants noted in the table as -03 or -07 Control were T₂ plants which did not contain the transgene under test (internal controls).

[00144] In event ME04249-03 all 11 transgene-containing plants exhibited the beneficial phenotypes. Event ME04249-07 had 5 transgene-containing plants which exhibited the beneficial phenotype and 2 transgene-containing plants which appeared wild-type. Our statistical analyses compared the internal controls to those plants with the beneficial phenotype which contained the transgene; all transgene-containing (as confirmed by PCR) but wild-type appearing plants were omitted from the statistical analyses in Table 10.

[00145] Segregation frequencies of the transgene under test suggest that each event contains a single insert, as calculated by a Chi-square test. Table 10 Quantitative phenotypes observed in 35S::cDNA 13495746 T₂ events

[00146] Summary of results:

• The ectopic expression of cDNA 13495746 with a strong constitutive promoter (35S) results in plants with thicker inflorescences, a larger rosette, and more rosette leaves.

• hi the events studied, the increase in plant size seen by this expression is accompanied by a delay in flowering time, but no reduction in fertility.

[00147] As a result, this gene/protein is especially useful for controlling the rate of cell divisions in meristems without disturbing overall plant morphology. It can be used in crops with an appropriate promoter to regulate size and growth rate of many individual organs. The protein may be used for creating sturdier stems in corn and preventing "snap". Increased vegetative biomass gives an improved source:sink ratio and improved fixation of carbon to sucrose and starch. Example 5: Lead 50; ME07495-03; ME07495-05; Ceres cDNA 12420535; clone

2835

[00148] Eight independently transformed events were selected and evaluated for their qualitative phenotype in the Ti generation as per standard protocol. Two events showing the most advantageous Ti phenotypes were chosen for evaluation in the T₂ generation. The T₂ growth conditions follow the above Ti protocol. The experimental design differs from the Ti planting in that each T₂ plant is contained within its own pot and no herbicide selection is used. All pots for each T₂ event are contained within the same flat, and the plants are randomly distributed within each flat. The controls for each set of measurements are the segregating progeny of the given Ti event which do not contain the T-DNA (internal controls). All analyses are done via soil-based experiments under long daylight conditions (16 hours) in the Ceres greenhouse.

[00149] This transgene produced a qualitative increase in overall plant size/biomass in 6 of 8 events with no fertility defects. These plants appeared to be delayed in flowering time by several days (Table 11). The transgenic "control" was a set of plants expressing a different 35S:cDNA fusion and were indistinguishable from the untransformed Ws wildtype.

Table 11. Qualitative phenotypes observed in 35S::cDNA 12420535 Ti events (all mutant phenotypes were equivalent, so the 2 highlighted events were randomly chosen for T₂ analyses).

[00150] Events ME07495-03 and ME07495-05 were evaluated in greater detail in the T₂ generation. Eighteen individuals for both events were sown and analyzed. Segregation frequencies of the plants under test suggest that each event contains a single insert, as calculated by a Chi-square test.

[00151] After detailed T₂ analyses, the following observations were determined regarding the transgenics (results below noted with a "*" are statistically significant to a 0.05 level or better via t-test unless otherwise noted):

• Flowering time (days to bolt) was approximately 6 days later than controls.

• Rosette leaf number at bolting was increased by approximately 3-4 leaves.

• Rosette area was approximately 3.5 times larger than controls.

• Height was increased approximately 20% (12 cm).

• Primary inflorescence thickness was increased approximately 30%.

[00152] Details can be found in Tables 12-13. Table 12. Quantitative phenotypes observed in 35S::cDNA 12420535 T₂ plants.

Table 13. Quantitative phenotypes observed in 35S::cDNA 12420535 T₂ plants.

[00153] Summary of results:

• The ectopic expression of cDNA 12420535 with a strong constitutive promoter (35S) results in taller plants with thicker inflorescences, larger rosettes, and more rosette leaves.

• The increase in plant size seen by this expression is accompanied by a delay in flowering time but no reduction in fertility.

[00154] As a result, this gene/sequence can provide Increased vegetative biomass to give an improved source:sink ratio to improve yield. Taller inflorescences give the opportunity for more flowers and, therefore, more seeds. The combination of improved biomass and inflorescence stature can give a significant improvement in yield. Thicker inflorescences can prevent "snap" caused by wind, rain, or drought.

Example 6: Lead 58; ME07957-01, 02 and -06; Ceres cDNA 1241656; clone 235672

[00155] Ten independently transformed events were selected and evaluated for their qualitative phenotype in the T₁ generation as per standard protocol. Three events showing the most advantageous Ti phenotypes were chosen for evaluation in the T₂ generation. The T₂ growth conditions follow the above Ti protocol. The experimental design differs from the T₁ planting in that each T₂ plant is contained within its own pot and no herbicide selection is used. All pots for each T₂ event are contained within the same flat, and the plants are randomly distributed within each flat. The controls for each set of measurements are the segregating progeny of the given Ti event which do not contain the T- DNA (internal controls). All analyses are done via soil-based experiments under long daylight conditions (16 hours) in the greenhouse.

[00156] This transgene produced an increase in overall plant size/biomass in 9 of 10 events with no fertility defects. These plants appeared to be delayed in flowering time by several days (Table 14). The transgenic "control" was a set of plants expressing a different 35S::cDNA fusion and were indistinguishable from the untransformed Ws wildtype (this method of scoring phenotypes is typical for our large-scale morphological phenotyping project).

Table 14. Qualitative phenotypes observed in 35S::cDNA 12414656 Ti events (all mutant phenotypes were equivalent, so the 3 highlighted events were randomly chosen for T₂ analyses).

[00157] Events ME07957-01, ME07957-02, and ME07957-06 were evaluated in greater detail in the T₂ generation. Eighteen individuals for each event were sown and analyzed. Segregation frequencies of the plants under test suggest that each event contains a single insert, as calculated by a Chi-square test.

[00158] After detailed T₂ analyses, we determined the following regarding the transgenics (results below noted with a "*" are statistically significant to a 0.05 level or better via t-test unless otherwise noted):

• Flowering time (days to bolt) was approximately 10 days later than controls.

• Rosette leaf number at bolting was increased by approximately 10 leaves.

• Rosette area was approximately 4.7 times larger than controls.

• Height was increased approximately 20% (12 cm).

• Primary inflorescence thickness was increased approximately 12%.

• Inflorescence number increased by approximately 2.1 more branches than controls. [00159] Details can be found in Tables 15-16.

[00160] Summary of results:

• The mis-expression of cDNA 12414656 with a strong constitutive promoter (35S) results in taller plants with thicker inflorescences, larger rosettes, and more rosette leaves.

• Since TxP experiments show that this gene is up-regulated under drought and SA application, this gene may be useful for stress tolerance.

[00161] As a result, this cDNA 12414656 can be used to increase vegetative biomass to give an improved source:sink ratio and improve yield. Taller inflorescences give the opportunity for more flowers and, therefore, more seeds. The combination of improved biomass and inflorescence stature can give a significant improvement in yield. Thicker inflorescences can prevent "snap" caused by wind, rain, or drought. This gene/protein can be especially useful for controlling the number/rate of cell divisions in meristems without disturbing overall plant morphology and could be developed in crops with an appropriate promoter to regulate size and growth rate of many individual organs.

Example 7 — Determination of Functional Homolog Sequences

[00162] The "Lead" sequences described in above Examples 1 - 6 are utilized to identify functional homologs of the lead sequences and, together with those sequences, are utilized to determine a consensus sequence for a given group of lead and functional homolog sequences.

[00163] A subject sequence is considered a functional homolog of a query sequence if the subject and query sequences encode proteins having a similar function and/or activity. A process known as Reciprocal BLAST (Rivera et al, Proc.Natl Acad. ScL USA ,1998, 95:6239-6244) is used to identify potential functional homolog sequences from databases consisting of all available public and proprietary peptide sequences, including NR from NCBI and peptide translations from Ceres clones.

[00164] Before starting a Reciprocal BLAST process, a specific query polypeptide is searched against all peptides from its source species using BLAST in order to identify polypeptides having sequence identity of 80% or greater to the query polypeptide and an alignment length of 85% or greater along the shorter sequence in the alignment. The query polypeptide and any of the aforementioned identified polypeptides are designated as a cluster.

[00165] The main Reciprocal BLAST process consists of two rounds of BLAST searches; forward search and reverse search. In the forward search step, a query polypeptide sequence, "polypeptide A," from source species S^A is BLASTed against all protein sequences from a species of interest. Top hits are determined using an E-value cutoff of 10^"5 and an identity cutoff of 35%. Among the top hits, the sequence having the lowest E-value is designated as the best hit, and considered a potential functional homolog. Any other top hit that had a sequence identity of 80% or greater to the best hit or to the original query polypeptide is considered a potential functional homolog as well. This process is repeated for all species of interest.

[00166] In the reverse search round, the top hits identified in the forward search from all species are used to perform a BLAST search against all protein or polypeptide sequences from the source species S^A. A top hit from the forward search that returned a polypeptide from the aforementioned cluster as its best hit is also considered as a potential functional homolog.

[00167] Functional homologs are identified by manual inspection of potential functional homolog sequences. Representative functional homologs are shown in Figures 1 - 5. Each Figure represents a grouping of a lead/query sequence aligned with the corresponding identified functional homolog subject sequences. Lead sequences and their corresponding functional homolog sequences are aligned to identify conserved amino acids and to determine a consensus sequence that contains a frequently occurring amino acid residue at particular positions in the aligned sequences, as shown in Figures 1-5.

[00168] Each consensus sequence then is comprised of the identified and numbered conserved regions or domains, with some of the conserved regions being separated by one or more amino acid residues, represented by a dash (-), between conserved regions.

[00169] Useful polypeptides of the inventions, therefore, include each of the lead and functional homolog sequences shown in Figures 1-5, as well as the consensus sequences shown in those Figures. The invention also encompasses other useful polypeptides constructed based upon the consensus sequence and the identified conserved regions. Thus, useful polypeptides include those which comprise one or more of the numbered conserved regions in each alignment table in an individual Figure depicted in Figures 1-5, wherein the conserved regions may be separated by dashes. Useful polypeptides also include those which comprise all of the numbered conserved regions in an individual alignment table selected from Figures 1-5, alternatively comprising all of the numbered conserved regions in an individual alignment table and in the order as depicted in an individual alignment table selected from Figures 1-5. Useful polypeptides also include those which comprise all of the numbered conserved regions in an individual alignment table and in the order as depicted in an individual alignment table selected from Figures 1-5, wherein the conserved regions are separated by dashes, wherein each dash between two adjacent conserved regions is comprised of the amino acids depicted in the alignment table for lead and/or functional homolog sequences at the positions which define the particular dash. Such dashes in the consensus sequence can be of a length ranging from length of the smallest number of dashes in one of the aligned sequences up to the length of the highest number of dashes in one of the aligned sequences.

[00170] Such useful polypeptides can also have a length (a total number of amino acid residues) equal to the length identified for a consensus sequence or of a length ranging from the shortest to the longest sequence in any given family of lead and functional homolog sequences identified in an individual alignment table selected from Figures 1-5.

[00171] The present invention further encompasses nucleotides that encode the above described polypeptides, as well as the complements thereof, and including alternatives thereof based upon the degeneracy of the genetic code.

[00172] The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims.

[00173] Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.

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Claims

CLAIMSWhat is claimed is:

1. An isolated nucleic acid molecule comprising:

(a) a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively ;

(b) a nucleotide sequence that is complementary to any one of the nucleotide sequences according to paragraph (a);

(c) a nucleotide sequence according to any one of SEQ ID Nos. 1, 9, 16, 21, 26 and 3;

(d) a nucleotide sequence that is in reverse order of any one of the nucleotide sequences according to (c) when read in the 5 ' to 3 ' direction;

(e) a nucleotide sequence that is an interfering RNA to the nucleotide sequence according to paragraph (a);

(f) a nucleotide sequence able to form a hybridized nucleic acid duplex with the nucleic acid according to any one of paragraphs (a) - (d) at a

temperature from about 40⁰C to about 48°C below a melting temperature

of the hybridized nucleic acid duplex;

(f) a nucleotide sequence encoding any one of the amino acid sequences identified as Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively; or

(g) a nucleotide sequence encoding any one of the lead, functional homolog or consensus sequences in Figures 1 - 5.

2. A vector, comprising: a) a first nucleic acid having a regulatory region encoding a plant transcription and/or translation signal; and a second nucleic acid having a nucleotide sequence according to any one the nucleotide sequences of claim 1, wherein said first and second nucleic acids are operably linked.

3. A method of modulating plant size, modulating vegetative growth, modulating plant architecture and/or modulating the plant biomass, said method comprising introducing into a plant cell an isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of :

temperature from about 40⁰C to about 48°C below a melting temperature

of the hybridized nucleic acid duplex; (f) a nucleotide sequence encoding any one of the amino acid sequences identified as Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively; or

(g) a nucleotide sequence encoding any one of the lead, functional homolog or consensus sequences in Figures 1 - 5, wherein said plant produced from said plant cell has modulated plant size, modulated vegetative growth, modulated plant architecture and/or modulated biomass as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid.

4. The method according to claim 3, wherein said consensus sequence comprises one or mor of the conserved regions identified in any one of the alignment tables in Figures 1-5.

5. The method according to claim 4, wherein said consensus sequence comprises all of the conserved regions identified in any onf of the alignment tables in Figures 1-5.

6. The method according to claim 5, wherein said consensus sequence comprises all of the conserved regions and in the order identified in any one of the alignment tables in Firgures 1-5.

7. The method according to claim 6, wherein said conserved regions are separated by gaps comprised of one or more amino acid residues.

8. The method according to claim 7, wherein each of said gaps is comprised of one or more amino acids consisting in number and kind of the amino acids depicted in the alignment table for the lead and/or functional homolog sequences at the corresponding positions that define said gap.

9. The method according to claim 8, wherein said consensus sequence has a length in terms of total number of amino acids that is equal to the length identified for a consensus sequence in one of Figures 1-5, or equal to a length reangin from the shortest to the longest sequence in any individual alignment table in any one of Figures 1-5.

10. The method of claim 3, wherein said difference is an increase in the level of plant size, vegetative growth, organ number and/or biomass.

11. The method of claim 3, wherein said isolated nucleic acid is operably linked to a regulatory region.

12. The method of claim 11 , wherein said regulatory region is a promoter selected from the group consisting of YP0092 (SEQ ID NO: ), PT0676 (SEQ ID NO: ), PT0708 (SEQ ID NO: ), PT0613 (SEQ ID NO: ), PT0672 (SEQ ID NO: ), PT0678 (SEQ ID NO: ), PT0688 (SEQ ID NO: ), PT0837 (SEQ ID NO: ), the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene, the soybean α' subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, and the barley hordein gene promoter.

13. The method of claim 11 , wherein said regulatory region is a promoter selected from the group consisting of p326 (SEQ ID NO:), YP0144 (SEQ ID NO:), YP0190 (SEQ ID NO:), pl3879 (SEQ ID NO:), YP0050 (SEQ ID NO:), p32449 (SEQ ID NO:), 21876 (SEQ ID NO:), YPO 158 (SEQ ID NO:), YP0214 (SEQ ID NO:X YP0380 (SEQ ID NO:), PT0848 (SEQ ID NO:), and PTO633 (SEQ ID NO:), the cauliflower mosaic virus (CaMV) 35 S promoter, the mannopine synthase (MAS) promoter, the 1' or 2' promoters derived from T-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, and ubiquitin promoters such as the maize ubiquitin-1 promoter.

14. The method of claim 11 , wherein said regulatory region is a promoter selected from the group consisting of ribulose-l,5-bisphosphate carboxylase (RbcS) promoters such as the RbcS promoter from eastern larch (Larix laricinά), the pine cabό promoter , the Cab-1 gene promoter from wheat , the CAB-I promoter from spinach, the cab IR promoter from rice ,the pyruvate orthophosphate dikinase (PPDK) promoter from corn, the tobacco Lhcbl *2 promoter, the Arabidopsis thaliana SUC2 sucrose-H+ symporter promoter, and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS, PT0535 (SEQ ID NO:), PT0668 (SEQ ID NO:), PT0886 (SEQ ID NO:), PR0924 (SEQ ID NO:), YPO 144 (SEQ ID NO:), YP0380 (SEQ ID NO:) and PT0585 (SEQ ID NO:),

15. A plant cell comprising an isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence encoding an amino acid sequence that is at least

85% identical to any one of Leads 11, 17, 50, 58, 13/64 and 12/67, corresponding to SEQ ID Nos. 2, 10, 17, 22, 27 and 4, respectively ;

temperature from about 40⁰C to about 48 °C below a melting temperature

16. A transgenic plant comprising the plant cell of claim 15.

17. Progeny of the plant of claim 16, wherein said progeny has modulated plant size, modulated vegetative growth, modulated plant architecture and/or modulated biomass as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid.

18. Seed from a transgenic plant according to claim 16.

19. Vegetative tissue from a transgenic plant according to claim 16.

20. A food product comprising vegetative tissue from a transgenic plant according to claim 16.

21. A feed product comprising vegetative tissue from a transgenic plant according to claim 16.

22. A product comprising vegetative tissue from a transgenic plant according to claim 16 used for the conversion into fuel or chemical feedstocks.

23. A method for detecting a nucleic acid in a sample, comprising: providing an isolated nucleic acid according to claim 1 ; contacting said isolated nucleic acid with a sample under conditions that permit a comparison of the nucleotide sequence of the isolated nucleic acid with a nucleotide sequence of nucleic acid in the sample; and analyzing the comparison.

24. A method for promoting increased biomass in a plant, comprising:

(a) transforming a plant with a nucleic acid molecule comprising a nucleotide sequence encoding any one of the lead, functional homolog or consensus sequences in any one of Figures 1-5; and (b) expressing said nucleotide sequence in said transformed plant, whereby said transformed plant has an increased biomass as compared to a plant that has not been transformed with said nucleotide sequence.

25. A method for modulating the biomass of a plant, said method comprising altering the level of expression in said plant of a nucleic acid molecule according to claim 1.