WO2016050512A1

WO2016050512A1 - Methods and means for increasing stress tolerance and biomass in plants

Info

Publication number: WO2016050512A1
Application number: PCT/EP2015/071214
Authority: WO
Inventors: Simon Barak; Vanessa RANSBOTYN; Matthew Hannah; Christoph VERDUYN
Original assignee: Bayer Cropscience Nv; B.G. Negev Technologies And Applications Ltd., At Ben-Gurion University
Priority date: 2014-10-03
Filing date: 2015-09-16
Publication date: 2016-04-07

Abstract

The present invention concerns a method for increasing stress tolerance and/or biomass comprising modulating the expression of any of the new abiotic stress regulator genes identified herein, as well as chimeric genes, nucleic acids and polypeptides encoding said genes. Also provided are plants or part thereof modulated according to the invention having an increased stress tolerance and/or biomass.

Description

Methods and means for increasing stress tolerance and biomass in plants

Field of the invention

[1 ] The present invention relates generally to the field of plant molecular biology and concerns a method for improving plant tolerance to stress conditions or for increasing plant growth rate or biomass. More specifically, the present invention concerns a method for increasing stress tolerance and/or growth rate and/or biomass comprising modulating the expression of any of the new abiotic stress regulator genes identified herein, as well as chimeric genes, nucleic acids and polypeptides or mutant alleles leading to reduced protein expression of said genes. Also provided are plants or part thereof modulated according to the invention having an increased stress tolerance and/or growth rate and/or biomass.

Background

[2] The requirement for food security for a rapidly increasing world population coupled with global climate change, as well as the need to use marginal land often located in harsh environments, is driving the demand for improved crop performance. Efforts have particularly focused on identifying genes important for traits such as yield, abiotic and biotic stress tolerance, and renewable energy. Although approaches for screening plant mutations, including both large-scale forward and reverse genetics have identified a number of agronomically important genes, such screens yield only a low frequency of desired phenotypes, typically <1 % - 3% of the individual mutants screened (Schneitz K, et al. (1997) Development 124(7): 1367-1376; Budziszewski GJ, et al. (2001 ) Genetics 159(4): 1765-1778; McElver J, et al. (2001 ) Genetics 159(4): 1751 -1763. Pagnussat GC, et al. (2005) Development 132(3): 603-614; Rama Devi S, et al. (2006) Plant J 47(4): 652-663; Kevei E, et al. (2006) Plant Physiol 140(3): 933-945; Koiwa H, et al.(2006) J Exp Bot 57(5): 1 1 19- 1 128; Dobritsa AA, et al. (201 1 ) Plant Physiol 157(2): 947-970). Such a low return is particularly problematic considering that screening populations can reach the tens of thousands to hundreds of thousands of plants (e.g. Rama 2006, supra, Koiwa 2006, supra). Such genetic screens are therefore time-consuming and expensive.

[3] To reduce the size of the screening population, an approach in recent years has been to employ computational biology to first identify a set of candidate genes and then to use reverse genetics to test mutants defective in those genes (d'Erfurth I, et al. (2008) PLoS Genet 4(1 1 ): e1000274; Usadel B, et al. (2009) Plant Cell Environ 32(12): 1633-1651 ; Fu et al. (2010) Plant Physiol 154: 927-938; Takenaka M, et al. (2010) J Biol Chem 285(35): 27122-27129). One novel computational strategy for prioritizing candidate genes is the network-guided genetic screen (NGGS) (Lan et al (2007) BMC Bioinformatics 8: 358; Bassel et al. (201 1 ) Proc Natl Acad Sci USA 108: 9709-9714; Bassel et al. (201 1 ) Plant Cell 23: 3101 -31 16; Bassel et al (2012) Plant Cell 24: 3859-3875; Tzfadia et al. (2012) Plant Cell 24: 43894406.Kim E, et al. (2010) Mol BioSyst 6(10): 1803-1806; Mutwil M, et al. (2010) Plant Physiol 152(1 ): 2943; Lee I, et al. (2010). Nat Biotechnol 28(2): 149-156; Lee I, et al. (201 1 ) Proc Natl Acad Sci USA 108(45): 18548-18553) whereby "omics' -derived datasets are employed to determine functional associations between connected genes (e.g. transcriptional co- expression, rule-based machine learning). These associations can be visualized as graphs (networks) in which nodes are genes and the edges are represented by values reflecting the significance of the functional association (e.g. a co- expression correlation coefficient) (Aoki K, et al.(2007) Plant Cell Physiol 48(3): 381 -390). One property of such networks is that highly connected clusters (modules) of genes that possess similar functions or participate in similar biological processes can be identified (Lee (2010), supra; Stuart J, (2003) Science 302(5643): 249-255; Lee H, et al. (2004) Genome Res 14(6): 1085-1094; Ficklin SP, et al. (2010) Plant Physiol 154(1 ): 13-24), and the function of unknown or unclassified genes present in a particular module can then be inferred - the guilt-by-association (GBA) principle (Usadel (2009) supra; Wolfe CJ, et al. (2005) BMC Bioinformatics 6: 227). The NGGS approach has not only reduced the number of mutants to be screened but several reports have demonstrated the possibility of improving the frequency of desired phenotypes (Lan (2007) supra; Bassel (201 1 ), supra; Mutwil (2010), supra; Lee (2010) supra; Lee 2001 , supra). For instance, diverse Arabidopsis thaliana functional genomics datasets (co-expression, protein-protein interactions, phylogenetic profiles etc.) were integrated to generate a probabilistic functional gene network - AraNet (Lee (2010), supra). This network was employed to generate a list of new candidate seed pigmentation genes and the resulting mutant screen showed a 10-fold increase in the hit rate (-15%) of desired phenotypes compared to screening random insertion mutants. In contrast to AraNet, a condition-specific microarray compendia examining transcriptome response in imbibed seeds was used to generate a co-expression network, SeedNet (Bassel 2001 , supra). Using GBA, mutants defective in genes representing uncharacterized hub nodes were screened and a 50% gene discovery rate was obtained. However, mutants of only eight of the highest ranked hub genes were screened. Indeed, apart from the AraNet study validating prediction of seed pigmentation genes, the few analyses that have validated their network predictions have only employed low numbers of mutants (Lan (2007), supra; Bassel (201 1 ), supra; Mutwil (2010), supra; Lee 2001 , supra) rendering it difficult to robustly assess gene discovery rate.

[4] Here, we combine an improved version of a novel gene expression ranking method that we developed (Kant P, et al. (2008) Plant, Cell Environ 31 (6): 697-714), with an mRNA co-expression network targeted to predict candidate genes regulating Arabidopsis responses to multiple abiotic stresses. To validate our predictions, we screened 62 mutants lines (including 2 alleles where available) defective in 42 candidate genes, for phenotypes under three different stresses. Our method led to a dramatically improved gene discovery rate of up to 62%. To further enhance the robustness of our analysis, we screened a further 53 mutants (64 lines) defective in genes assigned a gene rank but not present in the network and demonstrated that not only does the combination of gene ranking and co-expression network analysis increase gene discovery rate above that of gene ranking alone but it also allows prioritization of candidate genes for screening.

[5] There still remains a need for more methods for increasing stress tolerance and biomass in plants, as well as for nucleic acids and amino acid sequences for use therein. These are provided as described hereafter in the detailed description, the examples and the claims.

Summ ry

[6] In one embodiment, the invention describes a method for increasing the tolerance to stress conditions of a plant, plant part, plant cell or seed or for increasing growth rate and/or biomass of a plant, plant part, plant cell or seed, comprising the step of modulating the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[7] In another embodiment, said modulating the expression and/or activity of said protein comprises expressing in said plant, plant part, plant cell or seed a chimeric gene comprising the following operably linked elements:

a. A plant-expressible promoter.

b. A nucleic acid which when transcribed yields an RNA molecule that modulates the expression and/or activity of said protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 1 0, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

c. Optionally, a 3' end region functional in plants. [8] In another embodiment, said modulating the expression and/or activity of a protein comprises decreasing the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[9] In another embodiment, said RNA molecule decreases the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[10] In another embodiment, said RNA molecule comprises at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[1 1 ] In another embodiment, said RNA molecule comprises at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[12] In another embodiment, said RNA molecule comprises a sense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and an antisense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of said gene, wherein said sense and antisense region are capable of forming a double stranded RNA region comprising said at least 21 nucleotides.

[13] In another embodiment, said RNA region comprises at least 21 nucleotides having at least 76% sequence identity to a nucleotide sequence encoding a protein having at least 70% sequence identity to a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and/or at least 21 nucleotides having at least 76% sequence identity to the complement of said nucleotide sequence having at least 70% sequence identity to SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[14] In another embodiment, said RNA region comprises at least 21 nucleotides having at least 76% sequence identity to any one of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33 SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63, and/or at least 21 nucleotides having at least 76% sequence identity to the complement of any one of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33 SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63.

[15] In another embodiment, said decreasing the expression and/or activity comprises introducing into said plant, plant part, plant cell or seed a mutant or knock-out allele of a gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[16] In another embodiment, said stress condition is selected from salt stress, osmotic stress, ABA treatment, heat stress, drought stress.

[17] The invention also provides chimeric gene as described in any of the above methods.

[18] The invention also provides a mutant allele or knock-out allele of a gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58.

[19] The invention also provides a plant, plant part or plant cell comprising the chimeric gene or the mutant or knockout allele as described above.

[20] The invention also provides the use of the chimeric gene or the mutant allele as described above to produce a plant, plant part, plant cell or seed with increased stress tolerance and/or increased biomass.

Figure Legends

[21 ] Figure 1 : Hierarchical clustering of MST-scored gene expression in response to abiotic stresses demonstrates clustering of MST genes by stress. Hierarchical average linkage clustering was performed on the log2 signals from 6,025 probes designed for 6,005 MST-scored genes using an Arabidopsis ATH1 stress response microarray compendium. Close-up of heat (red) and osmotic and salt (turquoise) clades is shown. (B to D) Examples of organ-specific abiotic stress-responsive gene expression as revealed by hierarchical clustering and principal component analysis. Hierarchical average linkage clustering was performed on the log2 fold-change values from 6,025 probes designed for 6,005 MST- scored genes using Arabidopsis ATH1 cold (B) and osmotic stress (C) response microarrays. Hierarchical clustering with bootstrap analysis (n = 1 ,000) was carried out using The Institute for Genomic Research Multiple Experiment Viewer 3.1 (57). BP values are shown at branches. ABA, abscisic acid; C, cold stress, D, drought, H, heat; HH, high light, Os, osmotic stress; Ox, oxidative, Oz, ozone; S, salt, UV, U/V-B; R, root; S, shoot; Ro, rosette leaves; Se, seedling; cc, cell culture. Each array can be identified by its T-number that can be traced in Table S1. (D and E) Principal component analysis of MST-scored gene expression from cold (D) and osmotic stress microarrays (E). Each spot on the PCA plot represents one array. Organs, cell culture are color-coded according to the legend.

[22] Figure 2: Examples of organ-specific abiotic stress-responsive gene expression as revealed by hierarchical clustering and principal component analysis. (A, C) Hierarchical average linkage clustering was performed on the log2 fold-change values from 6,025 probes designed for 6,005 MST-scored genes using Arabidopsis ATH1 cold and osmotic stress response microarrays. Hierarchical clustering with bootstrap analysis (n = 1 ,000) was carried out using The Institute for Genomic Research Multiple Experiment Viewer 3.1 [57]. BP values are shown at branches. Os, osmotic stress; C, cold stress, R, root; S, shoot; Ro, rosette leaves; Se, seedling; cc, cell culture. Each array can be identified by its T-number that can be traced in Table S1 . (B, D) Principal component analysis (PCA) of MST-scored gene expression from osmotic and cold stress microarrays, respectively. Each spot on the PCA plot represents one array. Organs, cell culture are color-coded according to the legend.

[23] Figure 3: Distribution of correlation coefficients for MSTR genes associated with stress-related GO terms. (A, C) Spearman rank correlation coefficients (p < 0.01 ) were computed for MSTR genes associated with abiotic stress-specific parent and children GO biological process terms, using the root microarray compendium. (B, D) As a comparison, 1 ,000 gene lists equal in size to the MSTR gene set (n = 1 ,845) were randomly generated from the ATH 1 22k dataset. A subset of genes associated with the abiotic stress GO-terms were identified and Spearman rank correlation coefficients (p < 0.01 ) were calculated. The distribution of correlation coefficients from a representative randomly generated set closest in size to the respective MSTR gene set (e.g. Cold: MSTR, n = 45; random, n = 39) are shown in the figure. N-values in each graph are the number of significant edges.

[24] Figure 4: Effect of Spearman rank correlation coefficient threshold on size and homogeneity of modules from the root MSTR co-expression network. (A) Module size. (B) Module homogeneity. Modules were identified using the Matisse algorithm within Expander (Ulitsky, et al., 2010, Nat Protoc 5: 303-322). For box and whisker plots the median (thick black line) and interquartile range (IQR) of the observed differences are shown. Whiskers indicate the maximum/minimum range. Clear circles correspond to extreme observations with values greater than 1.5 times the IQR. n = number of modules.

[25] Figure 5: Use of MSTR gene co-expression networks for gene discovery based on guilt-by-association. (A) MSTR network modules are associated with specific abiotic stresses. Each graph represents one MSTR gene module. The average log2 fold-change expression of all genes in each module was calculated and plotted with Expander software [58]. Data are mean ± S.D. (B) First neighbors of the stress transcriptional regulator gene, DREB2A in the root network (r > ±0.85). Red edges, positive correlation; Blue edges, negative correlation; Genes in red, described in the literature as regulating one or more abiotic stress responses; Genes in black, candidate MSTR genes. The size of the node is proportional to the gene's MST score. (C) Union of shoot module 8 and root module 4 that are enriched with the GO term "response to abscisic acid stimulus. All edges represent positive correlations. Solid line, edge appears only in root network; red broken line, edge appears in both shoot and root networks; black broken line, edge appears only in shoot network. (D) Germination of a T-DNA insertion mutant of At3g57540 associated with the ABA-related module is insensitive to ABA compared to WT (Col-8).The ABA-insensitive mutant abil (also present in the module) was used as a positive control. Data are mean ± S.D. (n = 3). Each replicate plate contained ca. 40 seeds. Data are representative of similar results from two independent experiments where germination index of the mutant was significantly different (p < 0.05, linear mixed models) in response to 2 μΓτι ABA (Table 5).

[26] Figure 6: Discovery of novel MSTR genes regulating the response to salt and osmotic stresses. (A) Union of shoot and root network module 2 (shoot module 2, module MST score = 19.2; root module 2, module MST score = 18.8). (B) Enlargement of the three regions in module 2 showing the first neighbors of tested genes (green circles) ERF4A (At3g15210), HSFA4A (At4g18880) and NAC032 (At1 g77450). (C) Germination phenotypes of T-DNA insertion lines of At3g15210, At4g18880, At1 g77450 and their wild type control (Col-8) in response to salt stress (150 mM and 200 mM NaCI, red and green lines, respectively) and osmotic stress (250 mM and 500 mM mannitol, purple and orange lines, respectively). Blue lines, control MS plates; solid lines, wild-type; broken lines, mutant. Data are mean ± S.D. (n = 3). Each replicate plate contained ca. 40 seeds. Data are representative of similar results from two independent experiments where germination of the mutant was significantly different (p < 0.05, linear-mixed models) in at least one time point (Table 5).

[27] Figure 7: Discovery of novel MSTR genes regulating the response to heat stress. (A) Shoot network module 2 showing first neighbors of At1 g77450 (module MST score = 19.2). (B) Root module 2 showing first neighbors of At1 g73805 (module MST score = 18.8). (C, D) Cotyledon survival phenotypes of T-DNA insertion lines of At1 g77450 and At1 g73805 and their wild type control (Col 8) in response to heat stress (45 °C for 90 min and 150 min, red and green lines, respectively, and then returned to 22 °C for 5 d) Blue lines, control MS plates (22 °C); solid lines, wild-type (WT); broken lines, mutant. Data are mean ± S.D. (n = 4). Each replicate plate contained ca. 40 seeds. Data are representative of similar results in two independent experiments where cotyledon survival was significantly different (p < 0.05, linear- mixed models) in at least one time point (Table S4). (E) Cotyledon phenotype of At4g23130 (not in network) and its wild type control (Col 8) in response to heat stress. (F) Heat stress phenotype of At4g23130, five days after heat shock of 90 min).

[28] Figure 8: (A, B) The MST score can be employed to prioritize candidate genes only when used in combination with co-expression network analysis. (A) Receiver-Operator Characteristic (ROC) curves were used to measure true- positive phenotype rate (sensitivity; TP/(TP+FN)) versus false-positive rate (1 -specificity; FP/(FP+TN)) as a function of MST score. (B) Area under the ROC curve (AUC). The higher the value of the AUC, the better the performance of the MST score. P-values above each bar show that only the AUC for MSTR genes in the network is significantly (p < 0.05, asymptotic p-value for ROC curves) higher than random expectation.

(C, D) The contribution of co-expression network analysis to MST score-based screening of T-DNA insertion mutants for stress phenotypes (for combined network and non-network MSTR genes). (C) Receiver-Operator Characteristic (ROC) curves were used to measure true-positive phenotype rate (sensitivity; TP/(TP+FN)) versus false-positive rate (1 -specificity; FP/(FP+TN)) as a function of MST score. (D) Area under the ROC curve (AUC). The higher the value of the AUC, the better the performance of the MST score. P-values above each bar show that the AUC for the combined MSTR genes within and outside the network is significantly (p < 0.05) higher than random expectation. Results show that also for the combined set of network and non-network MSTR genes, the magnitude of the MST score can be employed to prioritize candidate genes only when used in combination with co-expression network analysis.

[29] Figure 9: Analysis of global network properties, (a) Shoot and root network degree distribution, (b) Shoot and root median clustering coefficient.

Detailed Description

[30] As challenges to food security increase, the demand for lead genes for improving crop production is growing. The identification of novel plant genes is essential for introducing new agricultural traits into crop plants. However, the screening of mutant plant populations for desired phenotypes (traits) is hampered by the low phenotypic hit rate (e.g. <1 % - 3%) thereby necessitating the use of thousands of plants. The availability of large datasets examining global gene expression allows us to take a computational systems biology approach to selecting a set of candidate genes likely to be involved in a particular biological process and then screening only those mutants defective in the candidate genes. Here, we present a method for selecting new regulators of plant abiotic stress responses that combines pre-selection of genes by ranking according to the number of stresses that regulate their expression, with analysis of gene co-expression over a large number of stress response experiments. By testing mutants in candidate genes for tolerance/sensitivity to different stresses, we are able to obtain a phenotypic hit rate of up to 62%. Furthermore, we are able to prioritize genes for screening according to their multiple stress ranking. Thus, future genetic screens in plants and other organisms can be targeted to other biological processes rendering screens less time-consuming, labor-intensive and expensive.

[31 ] The present invention has thus identified novel polypeptides and polynucleotides which can be used to modulate stress tolerance and/or biomass of a plant, plant part, plant cell or seed. By modulating the expression of the new abiotic stress regulator genes identified herein or functional homologues thereof, the stress tolerance and/or biomass of a plant, plant part, plant cell or seed can be modulated. Particularly, starting from the principle that T-DNA insertion leads to gene inactivation, stress tolerance and/or biomass of a plant, plant part, plant cell or seed can be increased by decreasing the transcript and/or protein expression of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to displays increased stress tolerance and/or growth rate and/or biomass in at least one of the below described assays (see e.g. Example 1 , Table 4, Example 7) when compared to control plants. Likewise, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed can be increased by increasing the transcript and/or protein expression of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutant were found to display decreased stress tolerance (i.e. increased stress sensitivity) and/or growth rate and/or biomass in at least one of the below described assays (see e.g. Example 1 , Table 4, Example 7) when compared to control plants.

[32] Thus, in a first embodiment, the invention describes a method for increasing the tolerance to stress conditions of a plant, plant part, plant cell or seed or for increasing biomass of a plant, plant part, plant cell or seed, comprising the step of modulating the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90. Optionally, this step is followed by the selection of a plant, plant part, plant cell or seed that has increased stress tolerance and/or increased biomass and/or increased growth rate as compared to control plants.

[33] As used herein "a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. X , i.e. of any of the above cited amino acid sequences, relates to a protein having the amino acid sequence of any of the above cited SEQ ID NOs, but also to functional variants of such proteins, e.g. proteins having at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any of the amino acid sequences cited above and having the same function and/or activity.

[34] In one embodiment, a protein having the activity of a protein having the amino acid sequence of any of the above amino acid sequences can be encoded by the nucleic acid sequence SEQ ID NO. 1 ., SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33 , SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63, SEQ ID NO. 65, SEQ ID NO. 67, SEQ ID NO. 69, SEQ ID NO. 71 , SEQ ID NO. 73, SEQ ID NO. 75, SEQ ID NO. 77, SEQ ID NO. 79, SEQ ID NO. 81 , SEQ ID NO. 83, SEQ ID NO. 85, SEQ ID NO. 87, SEQ ID NO. 89.

[35] The "sequence identity" of two related nucleotide or amino acid sequences, expressed as a percentage, refers to the number of positions in the two optimally aligned sequences which have identical residues (x100) divided by the number of positions compared. A gap, i.e., a position in an alignment where a residue is present in one sequence but not in the other, is regarded as a position with non-identical residues. The "optimal alignment" of two sequences is found by aligning the two sequences over the entire length according to the Needleman and Wunsch global alignment algorithm (Needleman and Wunsch, 1970, J Mol Biol 48(3):443-53) in The European Molecular Biology Open Software Suite (EMBOSS, Rice et al. , 2000, Trends in Genetics 16(6): 276—277; see e.g. http://www.ebi.ac.uk/emboss/align/index.html) using default settings (gap opening penalty = 10 (for nucleotides) / 10 (for proteins) and gap extension penalty = 0.5 (for nucleotides) / 0.5 (for proteins)). For nucleotides the default scoring matrix used is EDNAFULL and for proteins the default scoring matrix is EBLOSUM62.

Based on the available sequences, the skilled person can isolate homologous sequences or functional variants of the sequences disclosed herein using methods well known in the art, e.g., alignments, either manually or by using computer programs such as BLAST (Altschul et al. (1990), Journal of Molecular Biology, 215, 403410), which stands for Basic Local Alignment Search Tool or ClustalW (Thompson et al. (1994), Nucleic Acid Res., 22, 4673-4680) or any other suitable program which is suitable to generate sequence alignments.

[36] Homologous sequences as described above can comprise orthologous or paralogous sequences. Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. Three general methods for defining orthologous and paralogous genes are described; an ortholog, paralog or homolog may be identified by one or more of the methods described below. Orthologs and paralogs are evolutionarily related genes that have similar sequence and similar functions. Orthologs are structurally related genes in different species that are derived by a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event. Within a single plant species, gene duplication may result in two copies of a particular gene, giving rise to two or more genes with similar sequence and often similar function known as paralogs. A paralog is therefore a similar gene formed by duplication within the same species. Paralogs typically cluster together or in the same clade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLUSTAL (Thompson, et ah, (1994) Nucleic Acids Res. 22:4673-4680; Higgins, et al, (1996) Methods Enzymol. 266:383402). Groups of similar genes can also be identified with pair- wise BLAST analysis (Feng and Doolittle, (1987) J. Mol. Evol. 25:351 -360). Orthologous sequences can also be identified by a reciprocal BLAST strategy. Once an orthologous sequence has been identified, the function of the ortholog can be deduced from the identified function of the reference sequence. Orthologous genes from different organisms have highly conserved functions, and very often essentially identical functions (Lee, et al, (2002) Genome Res. 12:493-502; Remm, et al, (2001 ) J. Mol. Biol. 314:1041 -1052). Paralogous genes, which have diverged through gene duplication, may retain similar functions of the encoded proteins. In such cases, paralogs can be used interchangeably with respect to certain embodiments of the instant invention (for example, transgenic expression of a coding sequence).

[37] Functional variants or homologues of the sequences disclosed herein may also be identified and isolated by hybridization under stringent conditions using as probes identified nucleotide sequences or fragments thereof. For example, homologous sequences from other monocot species than the specific sequences disclosed herein are said to be substantially identical or essentially similar if they can be detected by hybridization under stringent, preferably highly stringent conditions. Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequences at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically stringent conditions will be chosen in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least 60°C. Lowering the salt concentration and/or increasing the temperature increases stringency. Stringent conditions for RNA-DNA hybridizations (Northern blots using a probe of e.g. 10Ont) are for example those which include at least one wash in 0.2X SSC at 63°C for 20min, or equivalent conditions.

[38] "High stringency conditions" can be provided, for example, by hybridization at 65°C in an aqueous solution containing 6x SSC (20x SSC contains 3.0 M NaCI, 0.3 M Na-citrate, pH 7.0), 5x Denhardfs (100X Denhardt's contains 2% Ficoll, 2% Polyvinyl pyrollidone, 2% Bovine Serum Albumin), 0.5% sodium dodecyl sulphate (SDS), and 20 \glm\ denaturated carrier DNA (single-stranded fish sperm DNA, with an average length of 120 - 3000 nucleotides) as non- specific competitor. Following hybridization, high stringency washing may be done in several steps, with a final wash (about 30 min) at the hybridization temperature in 0.2-0.1 ^χ SSC, 0.1 % SDS.

[39] "Moderate stringency conditions" refers to conditions equivalent to hybridization in the above described solution but at about 60-62°C. Moderate stringency washing may be done at the hybridization temperature in 1x SSC, 0.1 % SDS.

[40] "Low stringency" refers to conditions equivalent to hybridization in the above described solution at about 50- 52°C. Low stringency washing may be done at the hybridization temperature in 2x SSC, 0.1 % SDS. See also Sambrook et al. (1989) and Sambrook and Russell (2001).

[41 ] Other sequences corresponding to variants or homologues of the sequences disclosed herein may also be obtained by DNA amplification (PCR) using oligonucleotides specific for said sequences as primers, such as but not limited to oligonucleotides comprising or consisting of about 20 to about 50 consecutive nucleotides from the presently disclosed sequences and their complement. [42] Thus, in one embodiment, the modulating the expression and/or activity of a protein as described above comprises expressing in said plant, plant part, plant cell or seed a chimeric gene comprising the following operably linked elements:

a. A plant-expressible promoter.

b. A nucleic acid which when transcribed yields an RNA molecule that modulates the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

c. Optionally, a 3' end region functional in plants

thereby increasing the tolerance to stress conditions and/or increasing biomass of a plant, plant part, plant cell or seed.

[43] A chimeric gene, as used herein, refers to a gene that is made up of heterologous elements that are operably linked to enable expression of the gene, whereby that combination is not normally found in nature. As such, the term "heterologous" refers to the relationship between two or more nucleic acid or protein sequences that are derived from different sources. For example, a promoter is heterologous with respect to an operably linked nucleic acid sequence, such as a coding sequence, if such a combination is not normally found in nature. In addition, a particular sequence may be "heterologous" with respect to a cell or organism into which it is inserted (i.e. does not naturally occur in that particular cell or organism).

[44] The expression "operably linked" means that said elements of the chimeric gene are linked to one another in such a way that their function is coordinated and allows expression of the coding sequence, i.e. they are functionally linked. By way of example, a promoter is functionally linked to another nucleotide sequence when it is capable of ensuring transcription and ultimately expression of said other nucleotide sequence. Two proteins encoding nucleotide sequences, e.g. a transit peptide encoding nucleic acid sequence and a nucleic acid sequence encoding a protein according to the invention, are functionally or operably linked to each other if they are connected in such a way that a fusion protein of first and second protein or polypeptide can be formed.

[45] A gene, e.g. the chimeric gene of the invention, is said to be expressed when it leads to the formation of an expression product. An expression product denotes an intermediate or end product arising from the transcription and optionally translation of the nucleic acid, DNA or RNA, coding for such product, e. g. the second nucleic acid described herein. During the transcription process, a DNA sequence under control of regulatory regions, particularly the promoter, is transcribed into an RNA molecule. An RNA molecule may either itself form an expression product or be an intermediate product when it is capable of being translated into a peptide or protein. A gene is said to encode an RNA molecule as expression product when the RNA as the end product of the expression of the gene is, e. g., capable of interacting with another nucleic acid or protein. Examples of RNA expression products include inhibitory RNA such as e. g. sense RNA (co-suppression), antisense RNA, ribozymes, miRNA or siRNA, but also mRNA, rRNA and tRNA. A gene is said to encode a protein as expression product when the end product of the expression of the gene is a protein or peptide.

[46] As the skilled person will be well aware, various promoters may be used to promote the transcription of the nucleic acid of the invention, i.e. the nucleic acid which when transcribed yields an RNA molecule that modulates the expression and /or activity of a protein having the activity of a protein having any of the above amino acid sequences Such promoters include for example constitutive promoters, inducible promoters (e.g. stress-inducible promoters, drought-inducible promoters, hormone-inducible promoters, chemical-inducible promoters, etc.), tissue-specific promoters, developmental^ regulated promoters and the like.

[47] Thus, a plant expressible promoter can be a constitutive promoter, i.e. a promoter capable of directing high levels of expression in most cell types (in a spatio-temporal independent manner). Examples of plant expressible constitutive promoters include promoters of bacterial origin, such as the octopine synthase (OCS) and nopaline synthase (NOS) promoters from Agrobacterium, but also promoters of viral origin, such as that of the cauliflower mosaic virus (CaMV) 35S transcript (Hapster et al., 1988, Mol. Gen. Genet. 212: 182-190) or 19S RNAs genes (Odell et al., 1985, Nature. 6;313(6005):810-2; U.S. Pat. No. 5,352,605; WO 84/02913; Benfey et al., 1989, EMBO J. 8:2195-2202), the enhanced 2x35S promoter (Kay at al., 1987, Science 236: 1299-1302; Datla et al. (1993), Plant Sci 94:139-149) promoters of the cassava vein mosaic virus (CsVMV; WO 97/48819, US 7,053,205), 2xCsVMV (WO2004/053135) the circovirus (AU 689 31 1 ) promoter, the sugarcane bacilliform badnavirus (ScBV) promoter (Samac et al., 2004, Transgenic Res. 13(4):349-61 ), the figwort mosaic virus (FMV) promoter (Sanger et al., 1990, Plant Mol Biol. 14(3):433- 43), the subterranean clover virus promoter No 4 or No 7 (WO 96/06932) and the enhanced 35S promoter as described in US 5,164,316, US 5,196,525, US 5,322,938, US 5,359,142 and US 5,424,200. Among the promoters of plant origin, mention will be made of the promoters of the plant ribulose-biscarboxylase/oxygenase (Rubisco) small subunit promoter (US 4,962,028; W099/25842) from zea mays and sunflower, the promoter of the Arabidopsis thaliana histone H4 gene (Chaboute et al., 1987), the ubiquitin promoters (Holtorf et al., 1995, Plant Mol. Biol. 29:637-649, US 5,510,474) of Maize, Rice and sugarcane, the Rice actin 1 promoter (Act-1 , US 5,641 ,876), the histone promoters as described in EP 0 507 698 A1 , the Maize alcohol dehydrogenase 1 promoter (Adh-1 ) (from http://www.patentlens.net/daisy/promoters/242.html)). Also the small subunit promoter from Chrysanthemum may be used if that use is combined with the use of the respective terminator (Outchkourov et al., Planta, 216: 1003-1012, 2003). [48] A variety of plant gene promoters that regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner can be used for expression of a sequence in plants. Choice of a promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like.

[49] Additional promoters that can be used to practice this invention are those that elicit expression in response to stresses, such as the RD29 promoters that are activated in response to drought, low temperature, salt stress, or exposure to ABA (Yamaguchi-Shinozaki et al., 2004, Plant Cell, Vol. 6, 251 -264; WO12/101 1 18), but also promoters that are induced in response to heat (e.g., see Ainley et al. (1993) Plant Mol. Biol. 22: 13-23), light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1 : 471478, and the maize rbcS promoter, Schaffher and Sheen (1991 ) Plant Cell 3: 997-1012); wounding (e.g., wunl, Siebertz et al. (1989) Plant Cell 1 : 961 -968); pathogens (such as the PR-I promoter described in Buchel et al. (1999) Plant Mol. Biol. 40: 387-396, and the PDF 1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38: 1071 -1080), and chemicals such as methyl jasmonate or salicylic acid (e.g., see Gatz (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (e.g., see Gan and Amasino (1995) Science 270: 1986-1988); or late seed development (e.g., see Odell et al. (1994) Plant Physiol. 106: 447458).

[50] Use may also be made of salt-inducible promoters such as the salt-inducible NHX1 promoter of rice landrace Pokkali (PKN) (Jahan et al., 6^th International Rice Genetics symposium, 2009, poster abstract P4-37), the salt inducible promoter of the vacuolar ^-pyrophosphatase from Thellungiella halophila (TsVP1 ) (Sun et al., BMC Plant Biology 2010, 10:90), the salt-inducible promoter of the Citrus sinensis gene encoding phospholipid hydroperoxide isoform gpxl (Avsian-Kretchmer et al., Plant Physiology July 2004 vol. 135, p1685-1696).

[51 ] In alternative embodiments, tissue-specific and/or developmental stage-specific promoters are used, e.g., promoter that can promote transcription only within a certain time frame of developmental stage within that tissue. See, e.g., Blazquez (1998) Plant Cell 10:791 -800, characterizing the Arabidopsis LEAFY gene promoter. See also Cardon (1997) Plant J 12:367-77 , describing the transcription factor SPL3, which recognizes a conserved sequence motif in the promoter region of the A. thaliana floral meristem identity gene API; and Mandel (1995) Plant Molecular Biology, Vol. 29, pp 995-1004, describing the meristem promoter elF4. Tissue specific promoters which are active throughout the life cycle of a particular tissue can be used. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily only in cotton fiber cells, in one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily during the stages of cotton fiber cell elongation, e.g., as described by Rinehart (1996) supra. The nucleic acids can be operably linked to the Fbl2A gene promoter to be preferentially expressed in cotton fiber cells (Ibid) . See also, John (1997) Proc. Natl. Acad. Sci. USA 89:5769-5773; John, et al., U.S. Patent Nos. 5,608,148 and 5,602,321 , describing cotton fiber-specific promoters and methods for the construction of transgenic cotton plants. Root- specific promoters may also be used to express the nucleic acids of the invention. Examples of root-specific promoters include the promoter from the alcohol dehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. 123:39-60) and promoters such as those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186. Other promoters that can be used to express the nucleic acids of the invention include, e.g., ovule-specific, embryo-specific, endosperm-specific, integument- specific, seed coat-specific promoters, or some combination thereof; a leaf-specific promoter (see, e.g., Busk (1997) Plant J. 1 1 :1285 1295, describing a leaf-specific promoter in maize); the ORF 13 promoter from Agrobacterium rhizogenes (which exhibits high activity in roots, see, e.g., Hansen (1997) supra); a maize pollen specific promoter (see, e.g., Guerrero (1990) Mol. Gen. Genet. 224: 161 168); a tomato promoter active during fruit ripening, senescence and abscission of leaves, a guard-cell preferential promoter e.g. as described in PCT/EP12/065608, and, to a lesser extent, of flowers can be used (see, e.g., Blume (1997) Plant J. 12:731 746); a pistil-specific promoter from the potato SK2 gene (see, e.g., Ficker (1997) Plant Mol. Biol. 35:425 431 ); the Blec4 gene from pea, which is active in epidermal tissue of vegetative and floral shoot apices of transgenic alfalfa making it a useful tool to target the expression of foreign genes to the epidermal layer of actively growing shoots or fibers; the ovule-specific BELI gene (see, e.g., Reiser (1995) Cell 83:735-742, GenBank No. U39944); and/or, the promoter in Klee, U.S. Patent No. 5,589,583, describing a plant promoter region is capable of conferring high levels of transcription in meristematic tissue and/or rapidly dividing cells. Further tissue specific promoters that may be used according to the invention include: seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U .S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening (such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2AI 1 promoter (e.g., see U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (e.g., see Bird et al. (1988) Plant Mol. Biol. 1 1 : 651 -662), flower- specific promoters (e.g., see Kaiser et al. (1995) Plant Mol. Biol. 28: 231 -243), pollen-active promoters such as PTA29, PTA26 and PTAI 3 (e.g., see U.S. Pat. No. 5,792,929) and as described in e.g. Baerson et al. (1994 Plant Mol. Biol. 26: 1947-1959), promoters active in vascular tissue (e.g., see Ringli and Keller (1998) Plant Mol. Biol. 37: 977-988), carpels (e.g., see Oh l et al. (1990) Plant Cell 2:), pollen and ovules (e.g., see Baerson et al. (1993) Plant Mol. Biol. 22: 255- 267). In alternative embodiments, plant promoters which are inducible upon exposure to plant hormones, such as auxins, are used to express the nucleic acids used to practice the invention. For example, the invention can use the auxin- response elements El promoter fragment (AuxREs) in the soybean {Glycine max L.) (Liu (1997) Plant Physiol. 1 15:397- 407); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen (1996) Plant J. 10: 955-966); the auxin-inducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit (1997) Mol. Plant Microbe Interact. 10:933-937); and, the promoter responsive to the stress hormone abscisic acid (ABA) (Sheen (1996) Science 274:1900-1902). Further hormone inducible promoters that may be used include auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol. Biol. 39: 979-990 or Baumann et al., (1999) Plant Cell 1 1 : 323-334), cytokinin-inducible promoter (e.g., see Guevara-Garcia (1998) Plant Mol. Biol. 38: 743-753), promoters responsive to gibberellin (e.g., see Shi et al. (1998) Plant Mol. Biol. 38: 1053-1060, Willmott et al. (1998) Plant Molec. Biol. 38: 817-825) and the like. [52] In alternative embodiments, nucleic acids used to practice the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents which can be applied to the plant, such as herbicides or antibiotics. For example, the maize ln2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequence can be under the control of, e.g., a tetracycline-inducible promoter, e.g. , as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 1 1 :465 73); or, a salicylic acid-responsive element (Stange (1997) Plant J. 1 1 :1315-1324). Using chemically- {e.g. , hormone- or pesticide) induced promoters, i.e., promoter responsive to a chemical which can be applied to the transgenic plant in the field, expression of a polypeptide of the invention can be induced at a particular stage of development of the plant. Use may also be made of the estrogen-inducible expression system as described in US patent 6,784,340 and Zuo et al. (2000, Plant J. 24: 265-273) to drive the expression of the nucleic acids used to practice the invention.

[53] In alternative embodiments, a promoter may be used whose host range is limited to target plant species, such as corn, rice, barley, wheat, potato or other crops, inducible at any stage of development of the crop.

[54] In alternative embodiments, a tissue-specific plant promoter may drive expression of operably linked sequences in tissues other than the target tissue. In alternative embodiments, a tissue-specific promoter that drives expression preferentially in the target tissue or cell type, but may also lead to some expression in other tissues as well, is used.

[55] According to the invention, use may also be made, in combination with the promoter, of other regulatory sequences, which are located between the promoter and the coding sequence, such as transcription activators ("enhancers"), for instance the translation activator of the tobacco mosaic virus (TMV) described in Application WO 87/07644, or of the tobacco etch virus (TEV) described by Carrington & Freed 1990, J. Virol. 64: 1590-1597, for example.

[56] Other regulatory sequences that enhance the expression of the nucleic acid of the invention may also be located within the chimeric gene. One example of such regulatory sequences is introns. Introns are intervening sequences present in the pre-mRNA but absent in the mature RNA following excision by a precise splicing mechanism. The ability of natural introns to enhance gene expression, a process referred to as intron-mediated enhancement (IME), has been known in various organisms, including mammals, insects, nematodes and plants (WO 07/098042, p1 1 -12). IME is generally described as a posttranscriptional mechanism leading to increased gene expression by stabilization of the transcript. The intron is required to be positioned between the promoter and the coding sequence in the normal orientation. However, some introns have also been described to affect translation, to function as promoters or as position and orientation independent transcriptional enhancers (Chaubet-Gigot et al., 2001 , Plant Mol Biol. 45(1 ):17-30, p27-28). [57] Examples of genes containing such introns include the 5' introns from the rice actin 1 gene (see US5641876), the rice actin 2 gene, the maize sucrose synthase gene (Clancy and Hannah, 2002, Plant Physiol. 130(2):918-29), the maize alcohol dehydrogenase-1 (Adh-1 ) and Bronze-1 genes (Callis et al. 1987 Genes Dev. 1 (10):1 183-200; Mascarenhas et al. 1990, Plant Mol Biol. 15(6):913-20), the maize heat shock protein 70 gene (see US5593874), the maize shrunken 1 gene, the light sensitive 1 gene of Solanum tuberosum, and the heat shock protein 70 gene of Petunia hybrida (see US 5659122), the replacement histone H3 gene from alfalfa (Keleman et al. 2002 Transgenic Res. 1 1 (1 ):69- 72) and either replacement histone H3 (histone H3.3-like) gene of Arabidopsis thaliana (Chaubet-Gigot et al., 2001 , Plant Mol Biol. 45(1 ):17-30).

[58] Other suitable regulatory sequences include 5' UTRs. As used herein, a 5' UTR, also referred to as a leader sequence, is a particular region of a messenger RNA (mRNA) located between the transcription start site and the start codon of the coding region. It is involved in mRNA stability and translation efficiency. For example, the 5' untranslated leader of a petunia chlorophyll a/b binding protein gene downstream of the 35S transcription start site can be utilized to augment steady-state levels of reporter gene expression (Harpster et al., 1988, Mol Gen Genet. 212(1 ):182-90). WO95/006742 describes the use of 5' non-translated leader sequences derived from genes coding for heat shock proteins to increase transgene expression.

[59] The chimeric gene may also comprise a 3' end region, i.e. a transcription termination or polyadenylation sequence, operable in plant cells. As a transcription termination or polyadenylation sequence, use may be made of any corresponding sequence of bacterial origin, such as for example the nos terminator of Agrobacterium tumefaciens, of viral origin, such as for example the CaMV 35S terminator, or of plant origin, such as for example a histone terminator as described in published Patent Application EP 0 633 317 A1. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3' end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.

[60] Another measure to increase the expression of the nucleic acid of the invention that may be applied is optimizing the coding region for expression in the target organism, which may include adapting the codon usage , CG content, and elimination of unwanted nucleotide sequences (e.g. premature polyadenylation signals, cryptic intron splice sites, ATTTA pentamers, CCAAT box sequences, sequences that effect pre-mRNA splicing by secondary RNA structure formation such as long CG or AT stretches).

[61 ] Stress conditions, as used herein, refers e.g. to stress imposed by the application of chemical compounds (e.g., herbicides, fungicides, insecticides, plant growth regulators, adjuvants, fertilizers), exposure to abiotic stress (e.g., drought, waterlogging, submergence, high light conditions, high UV radiation, increased hydrogen peroxide levels, extreme (high or low) temperatures, ozone and other atmospheric pollutants, soil salinity or heavy metals, hypoxia, anoxia, osmotic stress, oxidative stress, low nutrient levels such as nitrogen or phosphorus etc.) or biotic stress (e.g., pathogen or pest infection including infection by fungi, viruses, bacteria, insects, nematodes, mycoplasms and mycoplasma like organisms, etc.). Stress may also be imposed by hormones such as ABA or compounds influencing hormone activity.

[62] Drought, salinity, extreme temperatures, high light stress and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755- 1767) describes a particularly high degree of "cross talk" between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up- regulation of anti-oxidants, accumulation of compatible solutes and growth arrest.

[63] A "control plant" as used herein is generally a plant of the same species which has wild-type levels of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90. "Wild-type levels" of a protein as used herein refers to the typical levels of said protein in a plant as it most commonly occurs in nature. Said control plant has thus not been provided either with a chimeric gene according to the invention nor with a mutant allele according to the invention (as described further below).

[64] Various methods are available in the art to measure the tolerance of plants, plant parts, plant cells or seeds to various stresses, some of which are described in the examples here below. Increased stress tolerance will usually be apparent from the general appearance of the plants and may be measured e.g., by increased biomass production, continued vegetative growth under adverse conditions or higher seed yield. Stress tolerant plants have a broader growth spectrum, i.e. they are able to withstand a broader range of climatological and other abiotic changes, without yield penalty, as compared to control plants. Biochemically, stress tolerance may be apparent as the higher NAD+-NADH /ATP content and lower production of reactive oxygen species of stress tolerant plants compared to control plants under stress condition. Stress tolerance may also be apparent as the higher chlorophyll content, higher germination rates, higher photosynthesis and lower chlorophyll fluorescence under stress conditions in stress tolerant plants compared to control plants under the same conditions. [65] It will be clear that it is also not required that the plant be grown continuously under the adverse conditions for the stress tolerance to become apparent. Usually, the difference in stress tolerance between a plant or plant cell produced according to the invention and a control plant or plant cell will become apparent even when only a relatively short period of adverse conditions is encountered during growth.

[66] Yield or biomass, as used herein, refers to seed number/weight, fruit number/weight, fresh weight, dry weight, leaf number/area, plant height, branching, boll number/size, fiber length, seed oil content, seed protein content, seed carbohydrate content. An increased growth rate as used herein refers to a period of increased growth or allocation to one or more of these cells or tissues that comprise the aforementioned plant organs.

[67] An increase in biomass or yield or growth can be an increase of at least 2%, or at least 5%, or at least 10%, or at least 15%, or at least 20%, or at least 25%, or at least 30%, or at least 40% , or at least 50%. Said increase is an increase with respect to biomass or yield or growth of control plants.

[68] Thus, a plant made according to the invention expressing a nucleic acid which when transcribed yields an RNA molecule that modulates the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90 can have at least one of the following phenotypes when compared to control plants, especially under adverse conditions (stress conditions), but also under control conditions, as described above, including but not limited to: increased overall plant yield, increased root mass, increased root length, increased leaf size, increased ear size, increased seed size, increased endosperm size, improved standability, alterations in the relative size of embryos and endosperms leading to changes in the relative levels of protein, oil and/or starch in the seeds, altered floral development, changes in leaf number, altered leaf surface, altered vasculature, altered intemodes, alterations in leaf senescence, absence of tassels, absence of functional pollen bearing tassels, or increased plant size when compared to a non-modified plant under normal growth conditions or under adverse conditions, such as water limiting conditions.

[69] In one aspect of the invention, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed is increased by decreasing the transcript and/or protein expression of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display increased stress tolerance and/or growth rate or biomass in at least one of the below described assays when compared to control plants (i.e. increased stress sensitivity) and/or growth rate and/or biomass in at least one of the below described assays (e.g. the stress conditions as listed in Table 4). Accordingly, in this aspect the modulating the expression and/or activity a protein as described above comprises decreasing the expression and/or activity in said plant, plant part, plant cell or seed of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

[70] An RNA molecule that results in a decreased expression and/or activity of a protein having the activity of a protein having any of the above amino acid sequences can be an RNA encoding a protein which inhibits expression and/or activity of said protein. Further, said RNA molecule can also be an RNA molecule which inhibits expression of a gene which is an activator of expression and/or activity of said protein. Said RNA molecule may also be an RNA molecule that directly inhibits expression and/or activity of a gene present in said plant, plant part, plant cell or seed encoding said protein, such as an RNA which mediates silencing of said gene.

[71 ] Decreasing the expression and/or activity of a protein having the activity of a protein having any of the above amino acid sequences can be decreasing the amount of functional protein produced. Said decrease can be a decrease with at least 30%, 40%, 50%, 60% , 70%, 80%, 90%, 95% or 100% (i.e. no functional protein is produced by the cell) as compared to the amount of functional protein produced by a cell with wild type expression levels and activity of said protein. Said decrease in expression and/or activity can be a constitutive decrease in the amount of functional protein produced. Said decrease can also be a temporal/inducible decrease in the amount of functional protein produced.

[72] The expression and/or activity of a protein having the activity of a protein having any of the above amino acid sequences can conveniently be reduced or eliminated by transcriptional or post-transcriptional silencing of the expression of the endogenous gene(s) present in said plant, plant part, plant cell or seed encoding said protein. To this end and within the chimeric gene described above, a silencing RNA molecule is introduced in the plant cells targeting the endogenous genes. As used herein, "silencing RNA" or "silencing RNA molecule" refers to any RNA molecule, which upon introduction into a plant cell, reduces the expression of a target gene. Such silencing RNA may e.g. be so-called "antisense RNA", whereby the RNA molecule comprises a sequence of at least 20 consecutive nucleotides having 95% sequence identity to the complement of the sequence of the target nucleic acid, preferably the coding sequence of the target gene. However, antisense RNA may also be directed to regulatory sequences of target genes, including the promoter sequences and transcription termination and polyadenylation signals. Silencing RNA further includes so-called "sense RNA" whereby the RNA molecule comprises a sequence of at least 20 consecutive nucleotides having 95% sequence identity to the sequence of the target nucleic acid. Other silencing RNA may be "unpolyadenylated RNA" comprising at least 20 consecutive nucleotides having 95% sequence identity to the complement of the sequence of the target nucleic acid, such as described in WO01 /12824 or US6423885 (both documents herein incorporated by reference). Yet another type of silencing RNA is an RNA molecule as described in WO03/076619 (herein incorporated by reference) comprising at least 20 consecutive nucleotides having at least 95%, at least 96%, at least 97% at least 98%, at least 99% or 100% sequence identity to the sequence of the target nucleic acid or the complement thereof, and further comprising a largely-double stranded region as described in WO03/076619 (including largely double stranded regions comprising a nuclear localization signal from a viroid of the Potato spindle tuber viroid-type or comprising CUG trinucleotide repeats). Silencing RNA may also be double stranded RNA comprising a sense and antisense strand as herein defined, wherein the sense and antisense strand are capable of base-pairing with each other to form a double stranded RNA region (preferably the said at least 20 consecutive nucleotides of the sense and antisense RNA are complementary to each other). The sense and antisense region may also be present within one RNA molecule such that a hairpin RNA (hpRNA) can be formed when the sense and antisense region form a double stranded RNA region. hpRNA is well-known within the art (see e.g WO99/53050, herein incorporated by reference). The hpRNA may be classified as long hpRNA, having long, sense and antisense regions which can be largely complementary, but need not be entirely complementary (typically larger than about 200 bp, ranging between 200-1000 bp). hpRNA can also be rather small ranging in size from about 30 to about 42 bp, but not much longer than 94 bp (see WO04/073390, herein incorporated by reference). An ihpRNA is an intron-containing hairpin RNA, which has the same general structure as an hpRNA, but the RNA molecule additionally comprises an intron in the loop of the hairpin that is capable of being spliced in the cell in which the ihpRNA is expressed. The use of an intron minimizes the size of the loop in the hairpin RNA molecule following splicing, and this increases the efficiency of interference. See, for example, Smith et al (2000) Nature 407:319-320. In fact, Smith et al, show 100% suppression of endogenous gene expression using ihpRNA-mediated interference. In some embodiments, the intron is the ADHI intron 1 . Methods for using ihpRNA interference to inhibit the expression of endogenous plant genes are described, for example, in Smith et al, (2000) Nature 407:319-320; Waterhouse and Helliwell, (2003) Nat. Rev. Genet. 4:29-38; Helliwell and Waterhouse, (2003) Methods 30:289-295 and US2003180945, each of which is herein incorporated by reference. A transient assay for the efficiency of hpRNA constructs to silence gene expression in vivo has been described by Panstruga, et al. (2003). The chimeric gene for hpRNA interference may also be designed such that the sense sequence and the antisense sequence do not correspond to an endogenous RNA. In this embodiment, the sense and antisense sequence flank a loop sequence that comprises a nucleotide sequence corresponding to all or part of the endogenous messenger RNA of the target gene present in the plant. Thus, it is the loop region that determines the specificity of the RNA interference. See, for example, WO0200904 herein incorporated by reference.

[73] A silencing RNA may also encode an artificial micro-RNA (miRNA) molecule as described e.g. in Schwab et al. 2006 (Plant Cell 18: 1 121 -1 133), WO2005/052170, WO2005/047505 or US 2005/0144667, or ta-siRNAs as described in WO2006/074400 (all documents incorporated herein by reference). MiRNAs are about 21 nucleotides in length and in plants up to 5 mismatches to their target sequence are allowed (Schwab et al. 2006, supra). [74] Within the chimeric genes of the invention, also amplicon chimeric genes can be used. Amplicon chimeric genes according to the invention comprise a plant virus-derived sequence that contains all or part of the target gene but generally not all of the genes of the native virus. The viral sequences present in the transcription product of the chimeric gene allow the transcription product to direct its own replication. The transcripts produced by the amplicon may be either sense or antisense relative to the target sequence. Methods of using amplicons to inhibit the expression of endogenous plant genes are described, for example, in US6635805, which is herein incorporated by reference.

[75] In some embodiments, the nucleic acid expressed by the chimeric gene of the invention is catalytic RNA or has ribozyme activity specific for the target sequence. Thus, the polynucleotide causes the degradation of the endogenous messenger RNA transcribed from the target gene/sequence, resulting in reduced expression of the protein present in the plant. This method is described, for example, in US4987071 , herein incorporated by reference.

[76] In one embodiment, the nucleic acid expressed by the chimeric gene of the invention encodes a zinc finger protein that binds to the gene encoding said protein, resulting in reduced expression of the target gene. In particular embodiments, the zinc finger protein binds to a regulatory region of said gene, thereby reducing gene transcription. In other embodiments, the zinc finger protein binds to the coding region thereby preventing its transcription. Methods of selecting sites for targeting by zinc finger proteins have been described, for example, in US6453242, and methods for using zinc finger proteins to inhibit the expression of genes in plants are described, for example, in US2003/0037355, each of which is herein incorporated by reference.

[77] In another embodiment, the nucleic acid expressed by the chimeric gene of the invention encodes a TALE protein that binds to a gene encoding said protein, resulting in reduced expression of the gene. In particular embodiments, the TALE protein binds to a regulatory region of said gene, thereby reducing gene transcription. In other embodiments, the TALE protein binds to the coding region thereby preventing its transcription. Methods of selecting sites for targeting by TALE proteins have been described in e.g. Moscou et al (2009, Science 326:1501 ) and Morbitzer et al (2010, Proc Natl Acad Sci USA 107:21617-21622).

[78] In another embodiment, the nucleic acid expressed by the chimeric gene of the invention encodes a CAS9- based repressor - guide RNA complex that binds to a gene encoding said protein, resulting in reduced expression of the gene. In particular embodiments, said complex binds to a regulatory region of said gene, thereby reducing gene transcription. In other embodiments, the complex binds to the coding region thereby preventing its transcription. How to modify the CRISPR/CAS system for use in targeted gene repression ("CRISPRi") is e.g. described in Mali et al.,(2013, Science 339: 823), US61/765576 and WO2013176772.

[79] In a further embodiment, the nucleic acid expressed by the chimeric gene of the invention encodes a nuclease, e.g. a meganuclease, zinc finger nuclease, TALEN, or CRISPR/CAS nuclease that specifically inactivates the endogenous target gene by recognizing and cleaving a sequence specific for said endogenous target gene. Using a template DNA, also specific mutations can be introduced into the gene. Chimeric genes encoding such nuclease can be removed afterwards by segregation.

[80] In some embodiments, to reduce or decrease the expression and/or activity of a protein having the activity of a protein having any of the above amino acid sequences (i.e. the target protein), a nucleic acid encoding an RNA molecule which is translated into a polypeptide can be introduced into a plant within the chimeric gene according to the invention, wherein the polypeptide is capable of reducing the expression and/or activity of said protein directly, i.e. the RNA molecule encodes an inhibitory protein or polypeptides.

[81 ] In one embodiment, such an inhibitory protein or polypeptide can be an antibody (including a nanobody etc) that binds to the target protein present in the plant and reduces the activity thereof. In another embodiment, the binding of the antibody results in increased turnover of the antibody complex by cellular quality control mechanisms. The expression of antibodies in plant cells and the inhibition of molecular pathways by expression and binding of antibodies to proteins in plant cells are well known in the art. See, for example, Conrad and Sonnewald, (2003) Nature Biotech. 21 :35-36, incorporated herein by reference.

[82] In another embodiment, such inhibitory protein or polypeptide may also be a dominant negative protein or protein fragment of the target protein.

[83] In an alternative embodiment, decreasing the expression and/or activity of a protein having the activity of a protein having any of the above amino acid sequences can be achieved by contacting the plant or plant cell with molecules interfering with the function of the endogenous protein present in the plant, e. g. by triggering aggregation of the target protein (interferor peptides) as e.g. described in WO2007/071789 and WO2008/148751 .

[84] In an even further embodiment, decreasing the expression and/or activity the target protein according to the invention can be achieved by contacting the plant or plant cell can with so-called alphabodies specific for said protein present in the plant, i.e. non-natural proteinaceous molecules that can antagonize protein function, as e.g. described in WO2009/030780, WO2010/066740 and WO2012/092970.

[85] In alternative embodiments, decreasing the expression and/or activity of protein having the activity of a protein having any of the above amino acid sequences can be achieved by inhibition of the expression of said protein present in the plant. Inhibition of the expression of said protein can be induced at the desired moment using a spray (systemic application) with inhibitory nucleic acids, such as RNA or DNA molecules that function in RNA-mediated gene silencing (similar to the above described molecules), as e.g. described in WO201 1/1 12570 (incorporated herein by reference).

[86] Thus, in a further embodiment, said RNA is a silencing RNA molecule, said molecule comprising: a. at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 present in said plant;

b. at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 present in said plant; or

c. a sense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and an antisense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of said gene present in said plant, wherein said sense and antisense region are capable of forming a double stranded RNA region comprising said at least 21 nucleotides.

[87] At least 76% sequence identity (e.g. 5 mismatches to the target sequence over a stretch of 21 consecutive nucleotides) in this respect can be at least 80% sequence identity (e.g. 4 mismatches over 21 nt), at least 85% sequence identity (e.g. 3 mismatches over 21 nt), at least 90% sequence identity (e.g. 2 mismatches over 21 nt), at least 95% sequence identity (e.g. 1 mismatch over 21 nt) or 100% sequence identity (no mismatches).

[88] As mentioned above, "a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. X" relates to a protein having the amino acid sequence of any of the above cited SEQ ID NOs, but also to functional variants of such proteins, e.g. proteins having at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any of the amino acid sequences cited above and having the same function and/or activity. [89] Thus, in a further embodiment, the gene present in said plant, plant part, plant cell or seed encodes a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64. Accordingly, the inhibitory RNA molecule may comprise at least 21 nucleotides having at least 76% sequence identity to a nucleotide sequence encoding a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and/or to the complement of such a nucleotide sequence.

[90] Accordingly, in an even further embodiment, the gene present in said plant, plant part, plant cell or seed encoding a protein having the activity of a protein having any of the above the amino acid sequences can have the nucleic acid sequence of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63. Accordingly, the inhibitory RNA molecule may comprise at least 21 nucleotides having at least 76% sequence identity to the nucleic acid sequence of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63 and/or to the complement of such a nucleic acid sequence.

[91 ] In again another embodiment, methods according the invention are provided wherein reducing the expression and/activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 comprises the step of introducing a knock-out allele of an endogenous gene encoding such a protein.

[92] A "knock-out allele" as used herein is an allele which is mutated as compared to the wild type allele (i.e. it is a mutant allele) and encodes a non-functional protein (i.e. a protein having no activity) or results in a significantly reduced amount of protein (by for example a mutation in a regulatory region such as the promoter), or which encodes a protein with significantly reduced activity. Said "knock-out allele" can be a mutant allele, which may encode no protein, or which may encode a non-functional protein or a protein with significantly reduced function, such as a mutant protein or a truncated protein. The allele may also be referred to as an inactivated allele.

[93] Said "significantly reduced amount of protein" can be a reduction in the amount (or levels) of protein produced by the cell comprising a knock-out allele by at least 30%, 40% , 50%, 60%, 70%, 80%, 90%, 95% or 100% (i.e. no protein is produced by the allele) as compared to the amount of the protein produced by the corresponding wild-type allele. The amount or level of a transcript (e.g. an mRNA) encoding a protein or the amount of level of a protein itself can be measured according to various methods known in the art such as (quantitative) RT-PCR, northern blotting, microarray analysis, western blotting, ELISA and the like.

[94] A "significantly reduced activity" can be a reduction in the activity of the protein produced by the cell comprising a knock-out allele of said protein by at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or 100% (i.e. no protein activity) as compared to the activity of the corresponding wild-type allele.

[95] A "wild-type allele" as used herein refers to a typical form of an allele as it most commonly occurs in nature, such as the alleles as represented by the nucleic acid sequence described in this application, e.g. of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[96] Basically, any mutation in the wild type nucleic acid sequences which results in a protein comprising at least one amino acid insertion, deletion and/or substitution relative to the wild type protein can lead to significantly reduced or no biological activity. It is, however, understood that certain mutations in the protein are more likely to result in a complete abolishment of the biological activity of the protein, such as mutations whereby significant portions of the functional domains are lacking. [97] A "mutant gene" or a "mutant allele" refers to a gene or allele comprising one or more mutations, such as a "missense mutation", a "nonsense mutation" or "STOP codon mutation" (including a mutation resulting in no functional protein ("knock-out allele of a gene"), an "insertion mutation", a "deletion mutation" or a "frameshift mutation" (the latter two including one or more mutations resulting in a "knock-out allele") with respect to the corresponding wild-type gene or allele, such as such as the genes and alleles as described in this application, e.g. as represented by SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[98] A nonsense mutation in an allele, as used herein, is a mutation in an allele whereby one or more translation stop codons are introduced into the coding DNA and the corresponding mRNA sequence of the corresponding wild type allele. Translation stop codons are TGA (UGA in the mRNA), TAA (UAA) and TAG (UAG). Thus, any mutation (deletion, insertion or substitution) that leads to the generation of an in-frame stop codon in the coding sequence will result in termination of translation and truncation of the amino acid chain. Thus, a full knockout mutant allele may comprise a nonsense mutation wherein an in-frame stop codon is introduced in the coding sequence by a single nucleotide substitution, such as the mutation of CAG to TAG, TGG to TAG, TGG to TGA, or CAA to TAA. Alternatively, a full knockout mutant allele may comprise a nonsense mutation wherein an in-frame stop codon is introduced in the coding sequence by double nucleotide substitutions, such as the mutation of CAG to TAA, TGG to TAA, or CGG to TAG or TGA. A full knockout mutant allele may further comprise a nonsense mutation wherein an in-frame stop codon is introduced in the coding sequence by triple nucleotide substitutions, such as the mutation of CGG to TAA. The truncated protein lacks the amino acids encoded by the coding DNA downstream of the mutation (i.e. the C-terminal part of the protein) and maintains the amino acids encoded by the coding DNA upstream of the mutation (i.e. the N-terminal part of the protein).

[99] A missense mutation in an allele, as used herein, is any mutation (deletion, insertion or substitution) in an allele whereby one or more codons are changed in the coding DNA and the corresponding mRNA sequence of the corresponding wild type allele, resulting in the substitution of one or more amino acids in the wild type protein for one or more other amino acids in the mutant protein.

[100] A frameshift mutation in an allele, as used herein, is a mutation (deletion, insertion, duplication of one or more nucleotides, and the like) in an allele that results in the nucleic acid sequence being translated in a different frame downstream of the mutation. [101 ] An "insertion mutation" is present if one or more melons have been added in the coding sequence of the nucleic acid resulting in the presence of one or more amino acids in the translated protein, whereas a "deletion mutation" is present if one or more codons have been deleted in the coding sequence of the nucleic acid resulting in the deletion of one or more amino acids in the translated protein.

[102] Said mutant allele can be introduced into said plant e. g. through mutagenesis. "Mutagenesis", as used herein, refers to the process in which plant cells are subjected to a technique which induces mutations in the DNA of the cells, such as contact with a mutagenic agent, such as a chemical substance (such as ethylmethylsulfonate (EMS), ethylnitrosourea (ENU), etc.) or ionizing radiation (neutrons (such as in fast neutron mutagenesis, etc.), alpha rays, gamma rays (such as that supplied by a Cobalt 60 source), X-rays, UV-radiation, etc.), T-DNA insertion mutagenesis (Azpiroz-Leehan et al. (1997) Trends Genet 13:152-156), transposon mutagenesis (McKenzie et al. (2002) Theor Appl Genet 105:23-33), or tissue culture mutagenesis (induction of somaclonal variations), or a combination of two or more of these. Thus, the desired mutagenesis of one or more genes or alleles may be accomplished by one of the above methods. While mutations created by irradiation are often large deletions or other gross lesions such as translocations or complex rearrangements, mutations created by chemical mutagens are often more discrete lesions such as point mutations. For example, EMS alkylates guanine bases, which results in base mispairing: an alkylated guanine will pair with a thymine base, resulting primarily in G/C to A/T transitions. Following mutagenesis, plants are regenerated from the treated cells using known techniques. For instance, the resulting seeds may be planted in accordance with conventional growing procedures and following pollination seed is formed on the plants. Additional seed that is formed as a result of such pollination in the present or a subsequent generation may be harvested and screened for the presence of mutant alleles. Several techniques are known to screen for specific mutant alleles, e.g., DeleteageneTM (Delete-a-gene; Li et al., 2001 , Plant J 27: 235-242) uses polymerase chain reaction (PCR) assays to screen for deletion mutants generated by fast neutron mutagenesis, TILLING (targeted induced local lesions in genomes; McCallum et al., 2000, Nat Biotechnol 18:455457) identifies EMS-induced point mutations, etc.

[103] Said mutant allele can also be introduced via gene targeting techniques. The term "gene targeting" refers herein to directed gene modification that uses mechanisms such as double stranded DNA break repair via non-homologous end-joining, homologous recombination, mismatch repair or site-directed mutagenesis. The method can be used to replace, insert and delete endogenous sequences or sequences previously introduced in plant cells. Methods for gene targeting can be found in, for example, WO 2006/105946 or WO2009/002150. Double stranded DNA breaks can be induced in a targeted manner using custom designed sequence specific nucleases and nuclease systems such as meganucleases/homing endonucleases, zinc finger nucleases, TALENs or CRISPR/CAS (for a review see Gaj et al., 2013, Trends Biotechnol 31 : 397405). In addition to making mutant alleles, such techniques can also be used to delete entire genes encoding proteins having the activity of a protein having any of the above amino acid sequences.

[104] Said mutant allele can also be introduced through introgression of a mutant allele into said plant. [105] In a further embodiment, stress tolerance and/or biomass of a plant, plant part, plant cell or seed is increased by decreasing the expression of two or more of the genes or functional homologues thereof of which the corresponding T- DNA insertion mutants were found to display increased stress tolerance and/or biomass compared to control plants. Accordingly, in this embodiment the modulating the expression and/or activity comprises decreasing the expression and/or activity of two or more (e.g. three, four, five etc) proteins having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, as described above.

[106] In a further embodiment, stress tolerance and/or biomass of a plant, plant part, plant cell or seed is increased by decreasing the expression of one or more of the genes or functional homologues thereof of which the corresponding T- DNA insertion mutants were found to display increased stress tolerance and/or biomass in at least two of the below described assays when compared to control plants.

[107] In an even further embodiment, stress tolerance and/or biomass of a plant, plant part, plant cell or seed is increased by decreasing the expression of one or more the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display increased stress tolerance and/or biomass in at least three or more of the below described assays when compared to control plants.

[108] In another aspect of the invention, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed is increased by increasing the expression of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display decreased stress tolerance (i.e. increased stress sensitivity) and/or growth rate and/or biomass in at least one of the below described assays (e.g. the stress conditions as listed in Table 4) when compared to control plants. Accordingly, in this aspect the modulating the expression and/or activity comprises increasing the expression and/or activity in said plant, plant part, plant cell or seed of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[109] In accordance with the present invention, the expression of any of the above proteins is increased if the transcript or protein level is statistically higher than the transcript or protein level of said protein in a plant that has not been modified to increase the expression of that protein. In particular embodiments of the invention, the transcript or protein level of the protein may be increased by more than 5%, more than 10%, more than 20%, more than 50%, more than 100%, more than 200% or even more when compared to the mRNA or protein level of the same gene in a plant that is not a mutant or that has not been modified to increase the expression of that protein. Expression of a transcript (e.g. an mRNA) or a protein can be measured according to various methods known in the art such as (quantitative) RT-PCR, northern blotting, microarray analysis, western blotting, ELISA and the like.

[1 10] In one embodiment, increasing the expression and/or activity of the protein having the activity of the protein of any of the above amino acid sequences involves expressing a nucleic acid which encodes protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[1 1 1 ] In a further embodiment, increasing the expression and/or activity of the protein having the activity of the protein of any of the above amino acid sequences involves expressing a nucleic acid nucleic acid encoding a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

[1 12] Such proteins may be encoded by a nucleic acid comprising the nucleotide sequence of SEQ ID NO. 65, SEQ ID NO. 67, SEQ ID NO. 69, SEQ ID NO. 71 , SEQ ID NO. 73, SEQ ID NO. 75, SEQ ID NO. 77, SEQ ID NO. 79, SEQ ID NO. 81 , SEQ ID NO. 83, SEQ ID NO. 85, SEQ ID NO. 87, SEQ ID NO. 89.

[1 13] Accordingly, in an even further embodiment, increasing the expression and/or activity of the protein having the activity of the protein of any of the above amino acid sequences involves expressing a nucleic acid comprising the nucleotide sequence of SEQ ID NO. 65, SEQ ID NO. 67, SEQ ID NO. 69, SEQ ID NO. 71 , SEQ ID NO. 73, SEQ ID NO.

75, SEQ ID NO. 77, SEQ ID NO. 79, SEQ ID NO. 81 , SEQ ID NO. 83, SEQ ID NO. 85, SEQ ID NO. 87, SEQ ID NO. 89.

[1 14] In a further embodiment, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed is increased by increasing the expression of two or more of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display decreased stress tolerance and/or biomass compared to control plants. Accordingly, in this embodiment the modulating the expression and/or activity comprises increasing the expression and/or activity of two or more (e.g. three, four, five etc.) proteins having the activity of a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO.

76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90 as described above.

[1 15] In a further embodiment, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed is increased by increasing the expression of one or more of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display decreased stress tolerance and/or biomass in at least two of the below described assays when compared to control plants.

[1 16] In an even further embodiment, stress tolerance and/or growth rate and/or biomass of a plant, plant part, plant cell or seed is increased by increasing the expression of one or more of the genes or functional homologues thereof of which the corresponding T-DNA insertion mutants were found to display decreased stress tolerance and/or biomass in at least three or at least four of the below described assays when compared to control plants.

[1 17] Increasing the expression of such a protein can conveniently be done by expressing in said plant, plant part, plant cell or seed a chimeric gene encoding such a protein. Such a chimeric gene can comprise the following operably linked elements:

a. A plant-expressible promoter

b. A nucleic acid which when transcribed and translated yields protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90

c Optionally, a 3' end region functional in plants

[1 18] Said chimeric gene can comprise any of the promoters, 3' end regions and additional elements as described above.

[1 19] In a further embodiment, increasing the expression and/or activity of the protein having the activity of the protein of any of the above amino acid sequences, can be achieved by modifying the endogenous gene(s) said protein. This can be done through, for example, T-DNA activation tagging, mutagenesis (e.g. EMS mutagenesis) or by targeted genome engineering technologies. Using such technologies for example, the endogenous promoter can be modified such that it drives higher levels of expression, or the endogenous promoter can be replaced with a stronger promoter, or mutations can be introduced into the coding region that enhance mRNA stability, translation efficiency, protein activity and/or stability, similar to the above described methods for enhancing the expression of the introduced chimeric gene.

[120] T-DNA activation tagging (Memelink, 2003, Methods Mol Biol. 236:345) is a method to activate endogenous genes by random insertion of a T-DNA carrying promoter or enhancer elements, which can cause transcriptional activation of flanking plant genes. The method can consist of generating a large number of transformed plants or plant cells using a specialized T-DNA construct, followed by selection for the desired phenotype.

[121 ] Targeted genome engineering refers to generating intended and directed modifications into the genome. Such intended modifications can be insertions at specific genomic locations, deletions of specific endogenous sequences, and replacements of endogenous sequences. Targeted genome engineering can be based on homologous recombination. Targeted genome engineering to increase the functional expression of a gene can consist of insertion of a promoter, stronger than the endogenous promoter, in front of the coding sequence, or insertion of an enhancer to increase promoter activity. Such techniques can also be applied e.g. to insert elements increasing RNA stability or enhancing translation of the encoded mRNA, or modify the coding sequence to enhance translation, protein stability and activity, similar to the above described methods for enhancing the expression of the introduced chimeric gene.

[122] The invention also provides chimeric genes comprising a nucleic acid which when transcribed yields an RNA molecule that modulates the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90 as described in detail above. Vectors comprising those chimeric genes are also included in the invention.

[123] Nucleic acids (i.e. chimeric genes and mutant alleles) used to practice the invention can be expressed by introduction into a plant cell by any means. For example, nucleic acids or expression constructs can be introduced into the genome of a desired plant host, or, the nucleic acids or chimeric genes can be episomes.

[124] "Introducing" in connection with the present application relates to the placing of genetic information in a plant cell or plant by artificial means, such as transformation. This can be effected by any method known in the art for introducing RNA or DNA into plant cells, tissues, protoplasts or whole plants. In addition to artificial introduction as described above, "introducing" also comprises introgressing genes or alleles as defined further below.

[125] Transformation means introducing a nucleotide sequence into a plant in a manner to cause stable or transient expression of the sequence. Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the selection of the most appropriate transformation technique will be determined by the practitioner. The choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods can include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium- mediated transformation. [126] In alternative embodiments, the invention uses Agrobacterium tumefaciens mediated transformation. Also other bacteria capable of transferring nucleic acid molecules into plant cells may be used, such as certain soil bacteria of the order of the Rhizobiales, e.g. Rhizobiaceae (e.g. Rhizobium spp., Sinorhizobium spp., Agrobacterium spp); Phyllobacteriaceae (e.g. Mesorhizobium spp., Phyllobacterium spp.); Brucellaceae (e.g. Ochrobactrum spp.); Bradyrhizobiaceae (e.g. Bradyrhizobium spp.), and Xanthobacteraceae (e.g. Azorhizobium spp.), Agrobacterium spp., Rhizobium spp., Sinorhizobium spp., Mesorhizobium spp., Phyllobacterium spp. Ochrobactrum spp. and Bradyrhizobium spp., examples of which include Ochrobactrum sp., Rhizobium sp., Mesorhizobium loti, Sinorhizobium meliloti. Examples of Rhizobia include R. leguminosarum bv, trifolii, R. leguminosarum bv,phaseoli and Rhizobium leguminosarum, bv, viciae (US Patent 7,888,552). Other bacteria that can be employed to carry out the invention which are capable of transforming plants cells and induce the incorporation of foreign DNA into the plant genome are bacteria of the genera Azobacter (aerobic), Closterium (strictly anaerobic), Klebsiella (optionally aerobic), and Rhodospirillum (anaerobic, photosynthetically active). Transfer of a Ti plasmid was also found to confer tumor inducing ability on several Rhizobiaceae members such as Rhizobium trifolii, Rhizobium leguminosarum and Phyllobacterium myrsinacearum, while Rhizobium sp. NGR234, Sinorhizobium meliloti and Mesorhizobium loti could indeed be modified to mediate gene transfer to a number of diverse plants (Broothaerts et al., 2005, Nature, 433:629-633).

[127] In alternative embodiments, making transgenic plants or seeds comprises incorporating sequences used to practice the invention and, in one aspect (optionally), marker genes into a target expression construct (e.g., a plasmid), along with positioning of the promoter and the terminator sequences. This can involve transferring the modified gene into the plant through a suitable method. For example, a construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. For example, see, e.g., Christou (1997) Plant Mol. Biol. 35:197-203; Pawlowski (1996) Mol. Biotechnol. 6:17-30; Klein (1987) Nature 327:70-73; Takumi (1997) Genes Genet. Syst. 72:63-69, discussing use of particle bombardment to introduce transgenes into wheat; and Adam (1997) supra, for use of particle bombardment to introduce YACs into plant cells. For example, Rinehart (1997) supra, used particle bombardment to generate transgenic cotton plants. Apparatus for accelerating particles is described U.S. Pat. No. 5,015,580; and, the commercially available BioRad (Biolistics) PDS-2000 particle acceleration instrument; see also, John, U.S. Patent No. 5,608,148; and Ellis, U.S. Patent No. 5, 681 ,730, describing particle-mediated transformation of gymnosperms.

[128] In alternative embodiments, protoplasts can be immobilized and injected with a nucleic acid, e.g., an expression construct. Although plant regeneration from protoplasts is not easy with cereals, plant regeneration is possible in legumes using somatic embryogenesis from protoplast derived callus. Organized tissues can be transformed with naked DNA using gene gun technique, where DNA is coated on tungsten microprojectiles, shot 1 /100th the size of cells, which carry the DNA deep into cells and organelles. Transformed tissue is then induced to regenerate, usually by somatic embryogenesis. This technique has been successful in several cereal species including maize and rice.

[129] In alternative embodiments, a third step can involve selection and regeneration of whole plants capable of transmitting the incorporated target gene to the next generation. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21 -73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee (1987) Ann. Rev. of Plant Phys. 38:467486. To obtain whole plants from transgenic tissues such as immature embryos, they can be grown under controlled environmental conditions in a series of media containing nutrients and hormones, a process known as tissue culture. Once whole plants are generated and produce seed, evaluation of the progeny begins.

[130] Viral transformation (transduction) may also be used for transient or stable expression of a gene, depending on the nature of the virus genome. The desired genetic material is packaged into a suitable plant virus and the modified virus is allowed to infect the plant. The progeny of the infected plants is virus free and also free of the inserted gene. Suitable methods for viral transformation are described or further detailed e. g. in WO 90/12107, WO 03/052108 or WO 2005/098004.

[131 ] In alternative embodiments, after the chimeric gene is stably incorporated in transgenic plants, it can be introduced into other plants by sexual crossing or introgression, as can a mutant allele according to the invention. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. Since transgenic expression of the nucleic acids of the invention leads to phenotypic changes, plants comprising the recombinant nucleic acids of the invention can be sexually crossed with a second plant to obtain a final product. Thus, the seed of the invention can be derived from a cross between two transgenic plants of the invention, or a cross between a transgenic or mutant plant of the invention and another plant. The desired effects (e.g., expression of the chimeric gene or mutant allele of the invention to produce a plant in stress tolerance is altered) can be enhanced when both parental plants express the chimeric genes or mutant alleles of the invention. The desired effects can be passed to future plant generations by standard propagation means.

[132] Successful examples of the modification of plant characteristics by transformation with cloned sequences which serve to illustrate the current knowledge in this field of technology, and include for example: U.S. Pat. Nos. 5,571 ,706; 5,677,175; 5,510,471 ; 5,750,386; 5,597,945; 5,589,615; 5,750,871 ; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,619,042. [133] In alternative embodiments, following transformation, plants are selected using a dominant selectable marker incorporated into the transformation vector. Such a marker can confer antibiotic or herbicide resistance on the transformed plants, and selection of transformants can be accomplished by exposing the plants to appropriate concentrations of the antibiotic or herbicide.

[134] In alternative embodiments, after transformed or mutated plants are selected and grown to maturity, those plants showing a modified trait are identified. The modified trait can be any of those traits described above. In alternative embodiments, confirmation that the modified trait is due to changes in expression levels or activity of the transgenic or mutated polypeptide or nucleic acid can be determined by analyzing mRNA expression using Northern blots, RT-PCR or microarrays, or protein expression using immunoblots or Western blots or gel shift assays.

[135] "Introgressing" means the integration of a gene or allele in a plant's genome by natural means, i.e. by crossing a plant comprising the chimeric gene or mutant allele described herein with a plant not comprising said chimeric gene or mutant allele. The offspring can be selected for those comprising the chimeric gene or mutant allele.

[136] The nucleic acids and polypeptides used to practice this invention can be expressed in or inserted in any plant cell, organ, seed or tissue, including differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, tumor tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.

[137] The invention further provides plants, plant cells, organs, seeds or tissues that have been modified so as to have a modulated expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90 when compared to a control plant. In particular, the invention provides plants, plant cells, organs, seeds or tissues that have been modified so as to have a reduced expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 when compared to a control plant. The invention further provides plants, plant cells, organs, seeds or tissues that have been modified so as to have an increased expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90 when compared to a control plant. These include for example transgenic or mutant plants or parts thereof, such as plant cells, organs, seeds or tissues, comprising and expressing the nucleic acids (chimeric genes or mutant alleles) used to practice this invention resulting in a modulated expression and/or activity of a protein having the activity of a protein having the amino acid sequence of any of the above sequences; for example, the invention provides plants, e.g., transgenic or mutant plants or parts thereof, such as, plant cells, organs, seeds or tissues that show improved tolerance to abiotic stress conditions, such as drought stress, osmotic stress, salt stress, heat stress, or that show reduced ABA sensitivity; thus, the invention provides stress-tolerant plants, plant cells, organs, seeds or tissues (e.g., crops). The invention also provides plants, e.g., transgenic or mutant plants or parts thereof such as plant cells, organs, seeds or tissues that show improved growth under control conditions; thus, the invention provides plants, plant cells, organs, seeds or tissues (e.g., crops) with increased biomass and/or yield and/or growth rate. The invention further provides plants, e.g., transgenic or mutant plants or parts thereof such as plant cells, organs, seeds or tissues that show improved growth under limiting water conditions; thus, the invention provides drought-tolerant plants, plant cells, organs, seeds or tissues (e.g., crops).

[138] A mutant plant, as used herein, refers to a plant comprising a mutant allele according to the invention.

[139] The plant, plant part, plant organs and plant cell of the invention comprising a nucleic acid (chimeric gene or mutant allele) used to practice this invention can be dicotyledonous (a dicot) or monocotyledonous (a monocot). Examples of monocots comprising a nucleic acid of this invention, e.g., as monocot transgenic plants of the invention, are grasses, such as meadow grass (blue grass, Poa), forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn). Examples of dicots comprising a nucleic acid of this invention, e.g., as dicot transgenic plants of the invention, are cotton, tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana. Thus, plant or plant cell comprising a nucleic acid of this invention, including the transgenic plants and seeds of the invention, include a broad range of plants, including, but not limited to, species from the genera Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Cojfea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannisetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solarium, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and Zea.

[140] The invention furthermore provides propagating material created from the plant of plants cells of the invention. The creation of propagating material relates to any means known in the art to produce further plants, plant parts or seeds and includes inter alia vegetative reproduction methods (e.g. air or ground layering, division, (bud) grafting, micropropagation, stolons or runners, storage organs such as bulbs, corms, tubers and rhizomes, striking or cutting, twin- scaling), sexual reproduction (crossing with another plant) and asexual reproduction (e.g. apomixis, somatic hybridization).

[141 ] In particular embodiments the plant cell described herein is a non-propagating plant cell, or a plant cell that cannot be regenerated into a plant, or a plant cell that cannot maintain its life by synthesizing carbohydrate and protein from the inorganics, such as water, carbon dioxide, and inorganic salt, through photosynthesis.

[142] The invention also provides the use of the chimeric gene or mutant allele according to the invention to produce a plant, plant part, plant cell or seed with increased stress tolerance or increased biomass. Also provided is the use of the plant according to the invention to produce a population of plants, such as crop plants with increased stress tolerance or increased biomass (e.g. increased yield).

[143] A nucleic acid or polynucleotide, as used herein, can be DNA or RNA, single- or double-stranded. Nucleic acids can be synthesized chemically or produced by biological expression in vitro or even in vivo. Nucleic acids can be chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Suppliers of RNA synthesis reagents are Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, CO, USA), Pierce Chemical (part of Perbio Science, Rockford, IL, USA), Glen Research (Sterling, VA, USA), ChemGenes (Ashland, MA, USA), and Cruachem (Glasgow, UK). In connection with the chimeric gene of the present disclosure, DNA includes cDNA and genomic DNA.

[144] The terms "protein" or "polypeptide" as used herein describe a group of molecules consisting of more than 30 amino acids, whereas the term "peptide" describes molecules consisting of up to 30 amino acids. Proteins and peptides may further form dimers, trimers and higher oligomers, i.e. consisting of more than one (poly)peptide molecule. Protein or peptide molecules forming such dimers, trimers etc. may be identical or non-identical. The corresponding higher order structures are, consequently, termed homo- or heterodimers, homo- or heterotrimers etc. The terms "protein" and "peptide" also refer to naturally modified proteins or peptides wherein the modification is effected e.g. by glycosylation, acetylation, phosphorylation and the like. Such modifications are well known in the art.

[145] As used herein "comprising" is to be interpreted as specifying the presence of the stated features, integers, steps or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps or components, or groups thereof. Thus, e.g., a nucleic acid or protein comprising a sequence of nucleotides or amino acids, may comprise more nucleotides or amino acids than the actually cited ones, i.e., be embedded in a larger nucleic acid or protein. A chimeric gene comprising a nucleic acid which is functionally or structurally defined, may comprise additional DNA regions etc.

[146] Unless stated otherwise in the Examples, all recombinant DNA techniques are carried out according to standard protocols as described in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, NY and in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R.D.D. Cray, jointly published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications, UK. Other references for standard molecular biology techniques include Sambrook and Russell (2001 ) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, NY, Volumes I and II of Brown (1998) Molecular Biology LabFax, Second Edition, Academic Press (U K). Standard materials and methods for polymerase chain reactions can be found in Dieffenbach and Dveksler (1995) PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, and in McPherson at al. (2000) PCR - Basics: From Background to Bench, First Edition, Springer Verlag, Germany.

[147] All patents, patent applications, and publications or public disclosures (including publications on internet) referred to or cited herein are incorporated by reference in their entirety.

[148] The sequence listing contained in the file named "BCS14-2009_ST25", which is 413 KB (size as measured in Microsoft Windows®), contains 90 sequences SEQ ID NO: 1 through SEQ ID NO: 90, is filed herewith by electronic submission and is incorporated by reference herein.

[149] The invention will be further described with reference to the examples described herein; however, it is to be understood that the invention is not limited to such examples.

Examples

Example 1 ; Experimen tal methods Preparation ofmicroarray datasets.

[150] CEL files from Affymetrix ATH1 22k datasets from experiments investigating WT Arabidopsis responses to various abiotic stresses were downloaded from either the Gene Expression Omnibus repository (Barrett T, et al. (2010). Nucleic Acids Res 39: D1005-D1010) or from ArrayExpress (Parkinson H, et al. (2007) Nucleic Acids Res 35: D747- D750.). All quality control and statistical calculations were performed using ROBIN software (Lohse M et al. (2010) Plant Physiol 153(2): 642-651 ). Quality control was assessed using all standard tests (e.g. M, MA, NUSE, RLE plots etc.) with default parameters. All arrays that exhibited a NUSE median < 1.1 were removed from further analysis. If only one replicate array remained after quality control, that treatment was discarded. Arrays were normalized using RMA. All arrays from the same experiment were analysed together and were compared to their respective control. Using ROBIN, a linear model and empirical Bayes method was used compute a moderated t-statistic in order to assess differential expression between control and all treatment conditions from a particular experiment. Multiple testing error rates were accounted for by using a false discovery rate (FDR) correction. A gene was considered to be stress-responsive if log2 fold-change expression was > 1 (p < 0.05) in at least one treatment within one experiment.

Construction of the stress database and identification of candidate MSTR genes.

[151 ] MST scores were calculated as described below in Example 2. Genes with an MST score < 6 (differentially expressed in less than three stresses) were removed and the remaining 6,005 genes were ranked based on their MST score. To compile a list of putative MSTR genes, the AGRIS (4), DATF (5) and PlantP (Gribskov M, et al. (2001 ) Nucleic Acids Res 29(1): 11 1 -113) databases were used to identify genes encoding regulatory proteins such as transcription factors, kinases and phosphatases. Other types of regulatory genes were extracted based on their MAPMAN bin code obtained with ROBIN. In total, 1 ,845 putative MSTR genes were identified representing -8% of the all non-control array identifiers on the ATHI chip.

Hierarchical clustering (HCA) and principal component analysis (PCA) of the MST dataset.

[152] The MST set of genes was subjected to HCA and PCA. For both analyses, the input matrix only contained average log2 fold-change expression values > 1 (p < 0.05) compared to each experiment's respective control (e.g. zero time point or control treatment). Hierarchical clustering (average linkage) using Pearson correlation with bootstrapping (n = 1 ,000 iterations) and PCA were computed and visualized using MEV 3.1 (Saeed Al, et al. (2003) Biotechniques 34(2) : 374-378). Based on the HCA and PCA results, we divided our microarray compendium into shoot and root datasets. Time points from the same stress treatment present in more than one experiment and/or from the same experiment were merged by their median, irrespective of different cell types from the same tissue (e.g. root collumella cell and root stele cell) or treatment level (e.g. heat 37 °C and 40 °C). This is because they grouped closely together in the HCA and PCA. Furthermore, outlier datasets from the cell culture experiment and one of the UV experiments that were located on isolated clades, were discarded.

Construction of gene co-expression networks.

[153] Log∑ transformed fold-change MSTR gene expression data from shoots and roots were used as the input matrix to generate coexpression networks. Gene expression similarity matrices were constructed for all genes across all treatments using the Spearman rank correlation metric. Network modules were identified by the Matisse algorithm within Expander (Ulitsky I, et al. (2010) Nat Protoc 5(2): 303-322.) with a minimum and maximum of 4 and 100 nodes, respectively, using varying Spearman rank correlation thresholds and homogeneity scores as described in the results. Box and whisker plots of module size/homogeneity vs. correlation coefficients were generated with R software (Version 2.15.1 ). Visualization of co-expression networks was performed with Cytoscape software (Cline MS et al. (2007). Nat Proto. 2(10): 2366-2382.). Identification of GO biological process/molecular function-enriched modules was carried out in Expander using the full MSTR gene list as background.

Evaluation of MSTR gene list.

[154] To examine the reliability of the functional associations (coexpression) between genes, we examined the distribution of correlation coefficients of MSTR genes with known abiotic stress GO biological process terms compared to genes associated with the same GO terms in 1 ,000 randomly generated set of genes equal in size to the MSTR gene set. Genes associated with specific GO abiotic stress terms (using only experimental evidence codes) were downloaded from the GO database (Ashburner M, et al. (2000) Nat Genet 25(1 ): 25-29.). The distribution of the correlation coefficients was plotted using the Statistical Pack for Social Sciences 19.0 software (SPSS Inc., Chigago IL). Random set generation, correlation test, and one-sample t-test between the MSTR gene sets and the 1 ,000 random sets, were performed using R software (version 2.15.1 ). For GO-term enrichment analysis of network modules, the TANGO software within the Expander software package (Ulitsky I, et al. (2010), supra) was used. TANGO performs hypergeometric enrichment tests corrected for multiple hypothesis testing by bootstrapping and estimating the empirical p-value distribution for the evaluated sets.

ROC curve analysis and discovery rate.

[155] Discovery rate was calculated as number of positive (stress phenotype) genes divided by number of genes tested. The probability of getting at least this number of positives was computed using the binomial distribution test with a probability of observing a positive gene set to 0.013, a value obtained by calculating the median discovery rate of several different large-scale screens of insertion mutants (Budziszewski GJ, et al. (2001 ) Genetics 159(4): 1765-1778; Rama Devi S, et al. (2006) Plant J 47(4): 652-663; Koiwa H,et al. (2006) J Exp Bot 57(5): 1 1 19-1 128; Dobritsa AA, et al. (201 1 ) Plant Physiol 157(2): 947-970 ;Takenaka M, et al. (2010) J Biol Chem 285(35): 27122-27129; Lee I, et al.(2010) Nat Biotechnol 28(2): 149-156). ROC curve analysis was applied to sets of tested genes as described in results. The genes within each set were ranked by their MST scores. AUC was computed using SPSS.

Plant material.

[156] All Salk T-DNA insertion mutants (Alonso JM, et al. (2003) Science 301 (5633): 653-657.) were obtained from the European Arabidopsis Stock Centre's (NASC) confirmed homozygote collection. For each mutant, seeds were bulked in parallel with WT Col-8 and hspl 01 control lines in a growth room at 20 °C, 70% relative humidity, and a photoperiod of 12 h light (225 μ moles photons m-2 s-1 )/12 h dark. To examine whether T-DNA insertion lines were indeed homozygous for the T-DNA insert, 10 lines that exhibited a stress phenotype were selected and then tested using gene-specific primers and a T-DNA-specific primer (Alonso et al., supra). Nine lines were found to be homozygote and one line was heterozygote (Table 1 ). All the homozygote lines exhibited a stress phenotype while the heterozygote showed no significant difference to wild-type.

Table 1 : Confirmation of homozygote plants by polymerase chain reaction

Abiotic Stress Assays.

[158] Abiotic stress assays were conducted according to (Kant P, et al (2007) Plant Physiol 145(3): 814-830) with some modifications. Approximately 40 to 50 surface-sterilized seeds were sown on plates containing MS salts, pH 5.8, 0.5 g L-1 MES, 0.8% (w/v) agar and either 2% (w/v) sucrose (heat stress assays) or no sucrose (salt and osmotic assays). Seeds were stratified at 4 °C for 4 d in the dark before being placed in a growth room at 22 °C, 50% relative humidity, and a photoperiod of 16 h light (150 μίηοΙ photons m-2s-1 )/8 h dark. For salt and osmotic stress or ABA response, MS medium was supplemented with various concentrations of NaCI, mannitol or ABA, respectively. Germination (emergence of radicals) and cotyledon emergence (green, fully-open cotyledons) were scored daily for 6 d until no further germination was observed. Germination was expressed either as percentage germination or germination index (a measure of germination rate) (Chiapusio G, et al. (1997) J Chem Ecol 23(1 1 ): 2445-2453). Three replicate plates were used per treatment. Basal thermotolerance assays were performed essentially according to (Bolle C (2009) ed Pfannschmidt T (Springer, Jena) 479: pp 1 -25). Seeds were allowed to germinate and seedlings were grown for 5 d after stratification in the growth room. Seedlings were heat-treated at 45 °C for differing periods of time and then returned to the growth room. Untreated seedlings left in the growth room were used as a control. Four plates were used per treatment, and survival (i.e. presence of green true leaves) was recorded daily for 5 d, at which point, survival had stabilized. At least two independent experiments for each stress assay were performed on all lines with different batches of seeds for several lines tested to remove any variability due to growth conditions of parental plants.

Statistical analysis.

[159] Statistical analyses of abiotic stress assays were performed with linear-mixed models using R (http://www.r- project.org). Where applicable, experiment, block and plate effects were included as random effects and contrasts of interest were made based on treatment, stress and genotype. A mutant line was considered to have a significant stress phenotype only when both independent experiments were significantly different from the wild type (p < 0.05).

Ranking of genes by MST score.

[160] MST scores were calculated as follows:

MST score = 2A +∑(B/B_C) where A is the number of distinct stresses in which a gene is differentially regulated, and Bi/Bc estimates the repeatability of the differential expression per stress, summed over the 10 stresses. A score of 1 was given for each stress type such that the A value of a gene that was up-/down-regulated under cold, salt and drought conditions would be 3; B, is the number of independent experiments of same stress in which gene expression is affected; B_c is the total number of experiments, above the first experiment, available for that stress. Bi/Bc is summed over the 10 stress treatments. The 2:1 ratio between the A and B gives weight to the effect on gene expression of different stresses while the B value represents a bonus for repeatability of microarray results.

Genes with an MST score < 6 (differentially expressed in less than three stresses) were removed and the remaining 6,005 genes were ranked based on their MST score.

Example 2; Selection of A rabidopsis Multiple Stress Regulatory (MSTR) genes for co- exp ressi o n a n a fys is

[161 ] In order to identify novel regulators of Arabidopsis responses to multiple abiotic stresses, we developed a Multiple Stress (MST) score that ranks genes according to the number of abiotic stresses that lead to a change in their microarray expression profile (Kant P, et al. (2008) F Plant, Cell Environ 31 (6): 697-714). A subset of these Multiple Stress (MST) genes, designated Multiple Stress Regulatory (MSTR) genes that encode regulatory proteins (transcription factors, kinases, phosphatases, etc.), can then be identified and we showed proof-of-concept by demonstrating that a mutant defective in the highest ranked MSTR gene exhibited sensitivity to multiple abiotic stresses. With the availability of vast amounts of abiotic stress transcriptome data that allow high resolution co-expression analysis, we hypothesized that co-expression analysis of a set of regulatory genes, pre-selected on the basis of their expression response to multiple abiotic stresses (MSTR genes), could be a powerful means of identifying novel abiotic stress regulators via an NGGS approach.

[162] To obtain a compendium of Arabidopsis abiotic stress microarrays, we downloaded Affymetrix microarray datasets from wild-type (WT) abiotic stress time course experiments. All datasets were subjected to a quality control and normalization pipeline with the final compendium comprising a total of 557 arrays representing 37 experiments and 10 stress treatments (ABA, cold, drought, heat, high light, osmotic, oxidative, ozone, salt, u/v). A set of 17,180 genes exhibiting > 2-fold absolute change in expression (p < 0.05) in at least one time point compared to control, in at least one stress experiment was identified for further analysis.

[163] To rank genes according to their stress-responsive expression, we improved our MST scoring system to take into account the greatly enlarged amounts of microarray data. The new MST score was derived from the following equation, which describes the degree of confidence that expression of a gene responds to multiple abiotic stresses: MST score = 2A +∑(B/B_C)

where A is the number of stress types in which a gene is differentially regulated. A score of 1 was given for each stress type such that the A value of a gene that was up-/down-regulated under cold, salt and drought conditions would be 3; B, is the number of independent experiments of same stress in which gene expression is affected; B_c is the total number of experiments, above the first experiment, available for that stress. Thus, the well-characterized DREB2A abiotic stress transcriptional regulator (Liu Q, et al. (1998) Plant Cell 10(8): 1391 -1406, Nakashima K, et al. (2000) Plant Mol Biol 42(4): 657-665) obtained a high MST score of 24.4 whereas the housekeeping gene UBQ10 obtained an MST score of zero. Because MSTR genes are likely to be upstream within stress signal transduction pathways, we only selected arrays representing time points up to 24 hours after application of stress, for MST scoring. We based this temporal window on the peak expression of known abiotic stress transcriptional activator genes, e.g. CBF/DREB, under different stresses (Kant et al., Plant Phys 145: 814-830, 2007). Because we were looking to identify multiple stress response genes, we determined a threshold cut-off MST score of 6; only genes that exhibited differential expression in response to at least three stress types (A = 3) would enter the list of MST genes. This analysis yielded a set of 6,005 MST genes with a threshold score > 6, out of which 1 ,845 encoded putative MSTR proteins (see Example 1 ).

Example 3; Evaluation of microarray compendium and M, led stress gene discovery

[164] The microarray compendium comprises diverse experiments from multiple stresses, different organs, developmental stages and even cell culture, which could lead to false positive associations between gene pairs. Thus, in order to examine whether we should generate a co-expression network from all or only part of the experimental data, we performed hierarchical clustering of MST gene expression over the whole microarray compendium (see Example 1 ). This analysis revealed that MST genes clustered by stress (Figure 1 ). We therefore carried out hierarchical clustering and Principal Component Analysis of MST genes for each stress separately, which revealed that within each stress, MST gene expression clustered by shoots and roots (Figure 2). This analysis further showed that experiments using cell culture clustered separately from shoots and roots and these experiments were therefore removed from the analysis. In light of these data, we decided to generate separate co-expression networks for shoots and roots.

[165] Because we intended to use GBA to assign biological process to genes according to co-expression with genes known to be involved in abiotic stress responses, it was important to show that the functional association (co -expression) between genes in our MSTR gene list was higher than expected by chance. We therefore selected all genes in the Arabidopsis genome associated with abiotic stress-specific parent and children Gene Ontology (GO) biological process terms (Ashburner M, et al. (2000) Nat Genet 25(1 ): 25-29) and then determined the distribution of Spearman rank correlation coefficients (p < 0.01 ) of those genes present in the MSTR gene list. As a comparison, a similar process was performed upon 1 ,000 randomly-generated gene lists of equal size to the MSTR gene list (n = 1 ,845 genes) from the ATH1 22k dataset. Root MSTR genes associated with the abiotic stress-related GO term "response to ABA" or "response to cold" and their children terms, possessed a much larger number of highly correlated connections than genes with the same GO biological process terms from randomly generated gene sets (Figure 3A-D). Thus, approximately 50% of root MSTR gene pairs associated with both GO-terms exhibited an absolute correlation above 0.5 compared to 25% and 27% of gene pairs from the 1 ,000 randomly generated lists for "response to ABA" and "response to cold", respectively (Figure 3E). Similar results were obtained for the shoot network (not shown). This enrichment of higher correlation coefficients in the MSTR gene list suggested an increased likelihood of detecting true abiotic stress regulators via GBA with known stress regulatory genes (Bhat P, et al. (2012) PLoS One 7(8): e39681.).

Example 4: Construction of MSTR gene co-expression networks, iden tifica tion of functional modules and selection of new candida te MSTR genes for abiotic stress screening

[166] Our next task was to construct MSTR co-expression networks that would allow us to identify gene modules with highly correlated expression thereby facilitating gene discovery by GBA (Wolfe CJ, et al. (2005) S BMC Bioinformatics 6: 227). However, partitioning networks such that there are a dense set of highly correlated edges within every module and few edges between modules depends upon the stringency of the co-expression metric. Therefore, to determine the optimal correlation coefficient for partitioning the MSTR networks, we examined the effect of different Spearman correlation coefficients (r) on the number of modules, module size (number of nodes) and homogeneity (average module correlation coefficient). Figure 4A shows that that increasing the r-threshold from 0.4 to 0.65 on the root MSTR network generated a small increase in the number of modules as more weakly co-expressed genes were removed and larger modules were split into smaller ones. However, the distribution of module size was skewed towards the maximum allowed module size of 100 nodes. Applying r > 0.65 led to a progressively reduced number of modules with fewer number of nodes per module as many weaker connections were removed but each module exhibited increased homogeneity scores (Figures 4A and B). Applying r = 0.8 reduced the number of modules to 15 but one module still contained the maximum allowed number of nodes. However, applying r = 0.85 generated the same number of modules but the amount of nodes in each module was below the maximum allowed. Moreover, the modules possessed a higher median homogeneity score than networks generated with lower r-values (Figures 4A and B). Similar results were obtained for the shoot network (not shown). Based on this analysis, we selected r≥ 0.85, which yielded 10 and 15 shoot and root modules, respectively (Table 3). The shoot MSTR network comprised 26 connected components with the largest connected component containing 70 nodes (genes). Together, the shoot network comprised 535 edges linking 236 nodes. The root MSTR network comprised 39 connected components with the largest connected component containing 66 nodes. Together, the root network comprised 382 edges linking 253 nodes. As expected, analyses of global network properties showed that the networks are small world and scale-free (Ravasz et al Methods Mol.Biol. 541 , 145-160, 2009) (Figure 9). Overall the modules comprised 360 distinct genes, a manageable number for selecting candidate genes for mutant screening.

[167] We next determined whether modules could be associated with particular functions. Firstly, we explored whether any of the modules were enriched in GO biological process and/or molecular function terms relative to the total MSTR gene set (p < 0.05, hyper-geometric enrichment corrected for multiple hypothesis testing) and found several such modules (Table 3). For instance, shoot module 8 and root module 4 showed enrichment of GO terms "response to abscisic acid stimulus" (71 % [p = 0.002, n = 7] and 77% [p = 0.001 , n= 9] of genes in the respective modules) and "response to water deprivation" (57% [p = 0.004] and 66% [p = 0.001 ] of genes in the respective modules). Shoot module 5 (n = 8) exhibited enrichment in the GO-term "response to auxin stimulus" (87% [p = 0.001 ] of module genes) while all eight genes of root module 7 were assigned the GO-term "nucleosome organization" (p = 0.001 ).

[168] Secondly, we examined whether any of the modules were associated with particular stresses by calculating the average expression profile of module genes in response to different abiotic stresses. This analysis revealed that many modules were indeed associated with specific stresses. For instance, genes in shoot modules 8 were up-regulated in response to ABA, salt and osmotic stresses, genes in shoot module 10 were up-regulated in response to osmotic and U/V stresses while genes in root module 5 were down-regulated in response to osmotic and heat stresses (Figure 5A, not shown).

[169] If GBA is to be applied, we expected that known stress regulatory genes would be directly connected to other known stress genes within a particular module. Inspection of the root network showed that well-characterized stress regulator genes such as the DREB2A transcription factor (Liu Q, et al. (1998) Plant Cell 10(8): 1391 -1406; Nakashima K, et al. (2000) Plant Mol Biol 42(4): 657-665.), is directly connected to 14 other well-known stress regulatory genes (Figure 5B). To further demonstrate the suitability of the network for GBA-based identification of new stress regulators, we inspected the modules for known stress regulatory genes that were tightly connected in a module containing gene of unknown function. The shoot and root "response to abscisic acid stimulus" modules possessed many common genes and a union of the two modules (Figure 5C) revealed that almost all genes in the united module were genes known to be involved in ABA signaling [34-38]. Only one gene, At3g57540 that encodes a remorin family protein, had no known function. Hence, to support the predictive power of the modules by GBA, we examined whether At3g57540 exhibited an ABA-dependent germination phenotype. Germination on ABA led to a 75% reduction in germination of wild-type seeds compared to the control (Figure 5D). On the other hand, At3g57540 seedlings showed an ABA insensitive phenotype and only displayed 52% reduction in germination, an even stronger phenotype than the classic ABA insensitive mutant, abi1 (Koornneef et al., 1989, Plant Physiol 90: 463469) that showed a 65% decrease in germination. Overall, these analyses demonstrated that functionally-associated genes could be detected in MSTR modules thereby increasing confidence that the MSTR gene co-expression network was suitable for GBA-based assigning of function to unknown genes.

[170] To generate a candidate MSTR gene list, we prioritized modules by calculating median module MST scores and choosing only those modules with a score > 10 (Table 2). This threshold module MST score represents genes whose expression is affected by at least 4 stresses but repeatable across multiple experiments of the same stress). Within these 16 modules, we further prioritized genes in the following order: (i) the module contains a known stress response gene(s); (ii) two independent homozygous T-DNA mutants available; (iii) one homozygous T-DNA mutant available; (iv) the module contains no known stress response gene. Table 2: Discovery rate (DR) of abiotic stress phenotypes in mutants defective in candidate MSTR genes

DR Fold-enrichment in DR

over classic genetic

screens

Network 0.62 48 (p = 1.2E-38)

Not in network 0.36 28 (p = 1.1 E-22)

Example 5: Mutan t screen of candida te Arabidopsis MSTR genes reveals previous}}' uniden tified ab iotic stress reg ula tors

[172] As mentioned above, almost all validation of plant network predictions have used low numbers of mutants. Therefore, to robustly validate the predictions of new Arabidopsis MSTR genes obtained via the combination of MST gene ranking and GBA-based co-expression network analysis, we screened 62 Arabidopsis T-DNA insertion mutant lines representing 42 MSTR genes, for sensitivity/tolerance to three different stresses - salt, osmotic or heat stress (Table 4). The data represent 345 experiments evaluating either germination (salt, osmotic) or seedling survival (heat). Examples of salt and osmotic stress-mediated germination mutant phenotypes are depicted in Figure 6. Germination of three mutant lines defective in genes from shoot and root modules 2 (Figure 6A and B) exhibited greater tolerance to salt and osmotic stress compared to wild-type suggesting that the genes may be new negative regulators of stress responses (Figure 6C). Evidence from several reports suggests that the genes defective in these mutants may be involved in abiotic stress responses: (i) AtERF4 is a negative regulator of ABA and ethylene responsive gene expression while ovenexpnession of BrERF4 from Brassica rapa in transgenic Arabidopsis generates stress tolerant plants (Yang Z, et al. (2005) Plant Mol. Biol. 58(4): 585-596; Seo, Y-J, et al. (2010) Mol Cells 30(3): 271 -277.); (ii) HSFA4A is a principal candidate H₂0₂ sensor during oxidative stress (Davletova S, et al. (2005) Plant Cell 17(1): 268-281 ; Miller G, Mittler R (2006) Ann Bot 98(2): 279-288; Scarped TE, et al. (2008) Plant Signal Behav 3(10): 856-857); (iii) NAC032 is a member of a large family of plant NAC genes, many of which have been shown to be involved in regulating abiotic stress responses (Nakashima K,et al. (2012; Biochim Biophys Acta 1819(2): 97-103).

[173] Examples of heat stress-mediated cotyledon survival mutant phenotypes are shown in Figure 7. Mutants defective in genes from shoot and root modules 2 (Figures 7A and B) exhibited greater thermotolerance indicating that the genes encoding SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1 ) and NAC032, are new negative regulators of the response to heat (Figures 7C and C). SARD1 has not previously been reported as being a regulator of heat stress. However, it is involved in the salicylic acid-mediated response to cold stress [Kim et al., 2013, Plant J doi: 10.11 11/tpj.12205]. Interestingly, the mutant defective in NAC032 was also tolerant to salt and osmotic stresses (Figure 6C) demonstrating that we were able to identify genes involved in regulating tolerance to multiple abiotic stresses.

Example 6: Evaluation of computational methods for selecting MSTR genes

[174] Of the 42 MSTR genes from the network, mutants of 26 genes exhibited a stress phenotype in at least one stress in two independent experiments yielding a discovery rate of 0.62 (Table 2). To compare this discovery rate with that obtained by other large-scale screens of insertional lines, the probability of getting at least this number of positives was computed using the binomial distribution test with a probability of observing a positive gene set to 0.013. This value was obtained by calculating the median discovery rate of several different large-scale screens of insertion mutants (Budziszewski et al., 2001 , . Genetics, 159, 1765-1778; Koiwa et al., 2006, Exp. Bot. 57, 11 19-1128; Rama Devi et al., 2006, Plant J. 47, 652-663; Lee et al., 2010, Nat. Biotechnol. 28, 149-156; Takenaka et al., 2010, Arabidopsis thaliana. J. Biol. Chem. 285, 27122-27129; Dobritsa et al., 2011 , Plant Physiol. 157, 947-970). This analysis revealed that the gene discovery rate of 0.62 achieved in our study represents a 48-fold (p < 10-37) enrichment in the discovery rate of a mutant phenotype compared to other large-scale screens. Notably, it was found that the gene discovery rate was not specific to the thresholds we used, and was remarkably stable over both gene and module MST threshold scores.

[175] Our method for identifying new MSTR genes combined MST gene ranking and co-expression network analysis and we wanted to evaluate the relative contribution of each component to the gene discovery rate. Therefore, we screened another 64 mutant lines representing 53 MSTR genes not present in the co-expression network (Example 1 ). An example of a heat stress phenotype of a non-network MSTR gene is shown in Figure 7E, This screen yielded a gene discovery rate of 0.36 representing a 28-fold (p < 10²¹; binominal distribution) enrichment in the discovery rate of a mutant phenotype compared to other large screens. The addition of the co-expression network analysis thus improved gene discovery rates by 1.7-fold (p = 5 x 10-4, binomial distribution) over discovery rates obtained by MST gene ranking alone. Nevertheless, it is notable that just ranking genes by MST score gave a relatively high gene discovery rate.

[176] It would clearly be an advantage to be able to prioritize screening of genes according to MST gene rank and we therefore asked whether MST rank alone facilitated such prioritization or whether it was necessary to combine MST gene ranking with the co-expression network analysis. To answer this question, we used Receiver-Operator Characteristic

(ROC) curves that measure true-positive phenotype rate versus false-positive rate as a function of MST score. The performance can be assessed by calculating the area under the curve (AUC), which is equal to the probability that the

MST score will rank a randomly chosen positive phenotype higher than a randomly chosen negative one. Figure 8AB shows that the value of the MST score had a significant effect (p = 0.003, asymptotic p-value for ROC curves) on the detection of a positive stress phenotype compared to random expectation for MSTR genes present in the network. However, the value of the MST score had no significant influence (p = 0.12) for MSTR genes not in the network. For analyses of non-network and network MSTR genes together, see Figure 8C-D. Thus, combining the MST score with co- expression network analysis not only considerably improves gene discovery rate but also allows prioritization of candidate genes according to MST rank.

Example 7: Further evaluation of newly identified MSTR genes

[177] A selection of mutants of the above MSTR genes are further evaluated for their stress phenotype as follows:

[178] Methods in vivo.

For each line (including WT) 60 seeds are sown in 5-6 cm pots, distributed across 20 trays and randomized. Following three days in the vernalisation room (4°C, dark), seeds are transferred to the growth chamber (22°C, 16/8 light/dark condition) and a plastic cover is maintained on the trays for one week. Before proceeding with the experiment quality control assessments are carried out including the assessment of germination percentage. At day 14 after stratification, water deficit treatment is applied. Half of the trays receive normal water regime and the other half are maintained at 7- 10% relative soil water content (measured daily using a WETsensor). The rosette diameter is measured on day 14, 28 and 42. At the end of the experiment (42 days), the fresh and dry weight of individual plants are also measured. The rosette diameter of the different lines is compared to the Col8 WT and presented as percentage difference.

[179] Phenopsis: automated watering and measurements.

For each line 28 seeds are sown in 8 cm pots, distributed and randomized in 14 plates (2 seeds per plate). Following three days in the stratification room (4°C, low light), seeds are transferred to the growth chamber (22°C, 16/8 light/dark condition) under high humidity (95% RH) for 4 days. Quality control assessments are carried out including the assessment of germination percentage and removal of weeds. At day 5 the humidity of the growth chamber is decreased to 65% RH. At day 14, water deficit treatment is applied. Half of the plants receive normal water regime (50% soil water content (SWC)) and the other half are maintained at 20% SWC (SWC is based on the weight of the pots). Visual picture are taken every day (until the 28th day) so that the plant diameter, compactness and area can be measured and compared to the Col8 WT and presented as percentage difference.

[180] Methods in vitro.

For in vitro stress assays, sorbitol (100mM) is used to investigate the effect of osmotic stress on the growth and performance of tested mutants. 14cm gridded petri dishes containing half MS medium (supplemented with 0.8% agar) are used. Seeds are sterilized using a vapor-phase method (for 1 h) and sown the day after on control and sorbitol- supplemented plates. The gridded plate is split into four to allow the sowing of four different lines. Eight seeds per lines are thus sown in each plate and this is replicated 10 times. In total 80 plants, for each line, are sown either on control or on sorbitol-supplemented medium. The plates are then stored in the dark at 4°C for three days. Following the stratification, plates are transferred to the growth chamber (22°C, 16/8 light/dark) and arranged following a randomized block design. To measure growth rate and biomass parameters, pictures are taken at 11 , 14, 16 and 18 day. The average area of the plants is measured and compared (at each time point) to that of the Col8 WT. The area and growth rate results are presented as percentage difference.

Example 8: Downregula tion using inhibitory RNAs

[181 ] The herein identified sequences or fragments thereof are cloned into a vector for downregulation of the endogenous gene as described elsewhere in this application (e.g. sense, antisense, hairpin or miRNA suppression) and transformed into plants, also as described elsewhere in this application. Downregulation of expression in the transformed plants is confirmed on the RNA and/or protein level. Plants are subjected to abiotic stress assays as described above. Plants are selected that have increased stress tolerance and/or that show increase growth rate or biomass as compared to control plants.

[182] Table 3: Details of GO-enrichment of gene modules from shoot and root MSTR co-expression networks

[183] Table 4: SALK T-DNA lines of candidate MSTR genes tested for abiotic stress germination phenotypes (To tolerant, Sen=sensitive, NS=not significant, ND=not determined)

Table 5: Statistical analysis (linear mixed models) of screen of Arabidopsis T-DNA insertion mutants for abiotic stress germination phenotypes (C=control,

M=manitol, N=NaCI, A=ABA, HS=heat shock, GI=germination index)

4 M250 At1 g77450a 97.3 99 0.810 98.3 99 0.953 3 N150 At4g 18880a 92.7 86 0.483 88 78.7 0.179

5 M250 At1 g77450a 98 99 0.882 98.3 99 0.944 4 N150 At4g 18880a 92.7 93.3 0.923 92 95.7 0.746

6 M250 At1 g77450a 98 99 0.891 98.3 99 0.945 5 N150 At4g 18880a 93.3 96 0.692 92 97.3 0.573

Gl M250 At1 g77450a 0.57 0.5 0.086 0.48 0.47 0.846 6 N150 At4g 18880a 93.3 96.7 0.649 92 97.3 0.585

1 M500 At1 g77450a 0 0 1.000 0 0 1 Gl N150 At4g 18880a 0.42 0.32 0.01 1 0.41 0.31 0.018

2 M500 At1 g77450a 0 0 1.000 0 0 1 1 N200 At4g 18880a 0 0 1.000 0.67 0 0.903

3 M500 At1 g77450a 20 1 0.048 4 1 0.664 2 N200 At4g 18880a 1 0 0.871 6.33 1 0.528

4 M500 At1 g77450a 69.7 6.33 0.000 41 .3 1 6E-04 3 N200 At4g 18880a 27 0 0.005 26 1 5E-04

5 M500 At1 g77450a 81 .7 1 1 .3 0.000 79 20.3 2E-08 4 N200 At4g 18880a 66 12.7 0.000 55 3.33 2E-05

6 M500 At1 g77450a 94.3 32 0.000 84 27 1 E-07 5 N200 At4g 18880a 84.3 28.7 0.000 75.3 40.3 4E-04

Gl M500 At1 g77450a 0.24 0.06 0.000 0.19 0.05 0.002 6 N200 At4g 18880a 89 56 0.000 83.3 61 0.024

1 N150 At1 g77450a 0 0 1.000 1 0 0.855 Gl N200 At4g 18880a 0.23 0.1 1 0.003 0.23 0.12 0.013

2 N150 At1 g77450a 37.7 4.33 0.000 22.7 1 0.012 1 C At5g39610a 96 95.7 0.948 77 92.7 0

3 N150 At1 g77450a 80 86 0.527 93.7 78.7 0.032 2 c At5g39610a 96.7 100 0.643 97.7 100 0.596

4 N150 At1 g77450a 89.3 93.3 0.563 97 95.7 0.906 3 c At5g39610a 96.7 100 0.664 97.7 100 0.683

5 N150 At1 g77450a 90.3 96 0.401 98.7 97.3 0.888 4 c At5g39610a 97.7 100 0.763 97.7 100 0.729

6 N150 At1 g77450a 90.3 96.7 0.388 98.7 97.3 0.891 5 c At5g39610a 97.7 100 0.760 97.7 100 0.612

Gl N150 At1 g77450a 0.35 0.32 0.378 0.36 0.31 0.202 6 c At5g39610a 97.7 100 0.633 97.7 100 0.32

1 N200 At1 g77450a 0 0 1.000 0 0 1 Gl c At5g39610a 0.97 0.98 0.733 0.87 0.96 0

2 N200 At1 g77450a 1 0 0.871 0.67 1 0.969 1 M250 At5g39610a 16.3 10.3 0.246 17 18 0.771

3 N200 At1 g77450a 22 0 0.022 5 1 0.563 2 M250 At5g39610a 75.3 90.7 0.035 55.3 79 0

4 N200 At1 g77450a 69.3 12.7 0.000 40 3.33 0.002 3 M250 At5g39610a 98.3 95 0.664 100 99 0.861

5 N200 At1 g77450a 80.7 28.7 0.000 80.3 40.3 6E-05 4 M250 At5g39610a 100 96 0.606 100 100 1

6 N200 At1 g77450a 87.3 56 0.000 85.3 61 0.014 5 M250 At5g39610a 100 96 0.600 100 100 1

Gl N200 At1 g77450a 0.23 0.1 1 0.004 0.19 0.12 0.082 6 M250 At5g39610a 100 96 0.413 100 100 1

1 C At3g 15210a 73.3 65.3 0.041 76.3 73.3 0.521 Gl M250 At5g39610a 0.54 0.52 0.654 0.51 0.55 0.034

2 c At3g 15210a 94.3 98.3 0.510 92 97.7 0.417 1 M500 At5g39610a 0 0 1.000 1 0 0.771

3 c At3g 15210a 94.3 100 0.460 92 97.7 0.573 2 M500 At5g39610a 1 0 0.889 6 7 0.82

4 C At3g 15210a 94.3 100 0.334 92 97.7 0.336 3 M500 At5g39610a 1 1 3.33 0.319 14.7 30 0.009

5 C At3g 15210a 94.3 100 0.314 92 97.7 0.432 4 M500 At5g39610a 42 23 0.016 47 76.3 0

6 c At3g 15210a 94.3 100 0.171 92 97.7 0.51 1 5 M500 At5g39610a 76.3 53.7 0.004 93.7 98.7 0.279

Gl c At3g 15210a 0.84 0.82 0.625 0.84 0.85 0.672 6 M500 At5g39610a 91 88 0.539 98.7 98.7 1

1 M250 At3g 15210a 23 1.67 0.000 1 1 1 .67 0.049 Gl M500 At5g39610a 0.21 0.18 0.376 0.24 0.27 0.208

2 M250 At3g 15210a 95 94 0.869 74.7 70.7 0.566 1 N150 At5g39610a 0 0 1.000 0 2.33 0.498

3 M250 At3g 15210a 96.7 96.7 1.000 87.7 98.7 0.275 2 N150 At5g39610a 5.33 14.7 0.196 7.67 10 0.596

4 M250 At3g 15210a 96.7 97.7 0.864 87.7 99.3 0.05 3 N150 At5g39610a 24.3 65.7 0.000 35.7 62.7 0

5 M250 At3g 15210a 97.7 98.3 0.905 88.7 99.3 0.141 4 N150 At5g39610a 73.3 91 .7 0.020 75.3 90 0.032

6 M250 At3g 15210a 97.7 98.3 0.871 88.7 99.3 0.217 5 N150 At5g39610a 93.7 91 .7 0.793 96 94.3 0.717

Gl M250 At3g 15210a 0.6 0.49 0.001 0.47 0.46 0.691 6 N150 At5g39610a 97 93.3 0.453 99.3 94.3 0.035

1 M500 At3g 15210a 0 0 1.000 0 0 1 Gl N150 At5g39610a 0.26 0.31 0.133 0.28 0.32 0.074

2 M500 At3g 15210a 17.7 0 0.004 0 0 1 1 N200 At5g39610a 0 0 1.000 0 0 1

3 M500 At3g 15210a 47 6.67 0.000 4.67 1 0.715 2 N200 At5g39610a 0 1 0.889 2 1 0.82

4 M500 At3g 15210a 62.7 25.3 0.000 30.3 14.3 0.008 3 N200 At5g39610a 7 7.33 0.965 6 7.67 0.77

5 M500 At3g 15210a 86.7 82 0.407 62.7 68.7 0.405 4 N200 At5g39610a 30.7 32 0.863 7 38.3 0

6 M500 At3g 15210a 90.3 90 0.935 90.3 94.7 0.615 5 N200 At5g39610a 54.3 76.3 0.005 30.3 87 0

Gl M500 At3g 15210a 0.28 0.2 0.006 0.19 0.19 0.973 6 N200 At5g39610a 67.7 89 0.000 68 95.3 0

1 N150 At3g 15210a 0 0 1.000 0 0 1 Gl N200 At5g39610a 0.15 0.2 0.190 0.13 0.21 0

2 N150 At3g 15210a 54 14.3 0.000 17.7 1 .67 0.024 1 C At5g47070a 84 99.3 0.031 80.3 40 5E-06

3 N150 At3g 15210a 81 .7 82.3 0.931 50.3 43.7 0.507 2 c At5g47070a 89 99.3 0.185 89.7 92.3 0.673

4 N150 At3g 15210a 86.7 93.3 0.256 79.3 85.3 0.308 3 c At5g47070a 92.3 100 0.123 92.3 96 0.61 1

5 N150 At3g 15210a 87.7 96 0.140 87.7 90.3 0.71 1 4 c At5g47070a 94 100 0.167 96.7 98 0.752

6 N150 At3g 15210a 87.7 96 0.045 87.7 92 0.615 5 c At5g47070a 94 100 0.025 98 98 1

Gl N150 At3g 15210a 0.38 0.33 0.130 0.29 0.26 0.588 6 c At5g47070a 94 100 0.019 98 98 1

1 N200 At3g 15210a 0 0 1.000 0 0 1 Gl c At5g47070a 0.88 0.99 0.009 0.87 0.68 5E-04

2 N200 At3g 15210a 1 1 .7 0 0.057 0 0 1 1 AO .5 At5g47070a 18 39.3 0.003 21 .7 9 0.121

3 N200 At3g 15210a 39.7 1 0.000 1 0 0.921 2 AO .5 At5g47070a 87.3 91 0.636 91 54.7 3E-07

4 N200 At3g 15210a 47 8.67 0.000 7.67 2.67 0.395 3 AO .5 At5g47070a 89 98.7 0.053 95.7 91 .7 0.579

5 N200 At3g 15210a 82.3 51 .3 0.000 39.3 15.3 0.001 4 AO .5 At5g47070a 90.7 98.7 0.067 95.7 92.3 0.431

6 N200 At3g 15210a 88.3 75 0.002 72 72 1 5 AO .5 At5g47070a 92.3 100 0.005 96.7 93.3 0.376

Gl N200 At3g 15210a 0.25 0.15 0.001 0.14 0.13 0.78 6 AO .5 At5g47070a 92.3 100 0.003 96.7 93.3 0.357

1 C At3g33066a 99.3 98 0.660 99.2 98 0.701 Gl AO .5 At5g47070a 0.54 0.68 0.002 0.58 0.45 0.014

2 c At3g33066a 99.3 98.7 0.891 99.2 98.7 0.919 1 A2.0 At5g47070a 0 2.67 0.703 0 1 0.902

3 c At3g33066a 99.3 98.7 0.871 99.2 98.7 0.903 2 A2.0 At5g47070a 4.33 6.67 0.763 2.33 7.67 0.399

4 c At3g33066a 99.3 98.7 0.952 99.2 98.7 0.964 3 A2.0 At5g47070a 17 20 0.543 44.3 39.3 0.489

5 c At3g33066a 99.3 98.7 0.951 99.2 98.7 0.963 4 A2.0 At5g47070a 46 52.3 0.145 80 82.7 0.528

6 c At3g33066a 99.3 98.7 0.926 99.2 98.7 0.944 5 A2.0 At5g47070a 82.3 93.3 0.000 85.3 85.3 1

Gl c At3g33066a 0.99 0.98 0.656 0.99 0.98 0.715 6 A2.0 At5g47070a 84.3 94.3 0.000 86.7 85.3 0.712

1 M250 At3g33066a 4.33 14.3 0.001 4.3 14.3 0.001 Gl A2.0 At5g47070a 0.21 0.26 0.312 0.25 0.26 0.896

2 M250 At3g33066a 96.7 95.7 0.837 96.6 95.7 0.842 1 C At4g26080a 97 99.3 0.738 91 .7 40 3E-08

3 M250 At3g33066a 98.7 96.7 0.627 98.4 96.7 0.682 2 C At4g26080a 97 99.3 0.763 93.3 92.3 0.874

4 M250 At3g33066a 98.7 97.3 0.904 98.4 97.3 0.927 3 C At4g26080a 97 100 0.543 95.7 96 0.963

5 M250 At3g33066a 98.7 98.3 0.976 98.4 98.3 0.999 4 C At4g26080a 98 100 0.643 95.7 98 0.581

6 M250 At3g33066a 98.7 98.3 0.963 98.4 98.3 0.998 5 C At4g26080a 98 100 0.447 95.7 98 0.534

Gl M250 At3g33066a 0.51 0.56 0.081 0.51 0.56 0.1 16 6 C At4g26080a 98 100 0.423 95.7 98 0.518

1 M500 At3g33066a 0 0 1.000 0 0 1 Gl c At4g26080a 0.97 0.99 0.623 0.93 0.68 1 E-05

2 M500 At3g33066a 0 0 1.000 0 0 1 1 A2.0 At4g26080a 0 2.67 0.703 6.33 1 0.51 1

3 M500 At3g33066a 1 3.33 0.571 0.83 3.33 0.543 2 A2.0 At4g26080a 36.7 6.67 0.000 39 7.67 6E-06

4 M500 At3g33066a 30.3 56.7 0.019 30 56.7 0.018 3 A2.0 At4g26080a 68.7 20 0.000 81 39.3 3E-07

5 M500 At3g33066a 68.7 85.3 0.127 68.3 85.3 0.121 4 A2.0 At4g26080a 74 52.3 0.000 87.3 82.7 0.272

6 M500 At3g33066a 79.3 94.3 0.038 79.2 94.3 0.036 5 A2.0 At4g26080a 89.7 93.3 0.165 87.3 85.3 0.594

Gl M500 At3g33066a 0.17 0.22 0.095 0.17 0.22 0.091 6 A2.0 At4g26080a 91 .3 94.3 0.231 87.3 85.3 0.58

1 N150 At3g33066a 0 0 1.000 0 0 1 Gl A2.0 At4g26080a 0.34 0.26 0.064 0.38 0.26 0.025

2 N150 At3g33066a 23.3 39.7 0.001 23.3 39.7 0.001 1 C At3g57540a 98.3 99.3 0.886 96.7 40 2E-09

3 N150 At3g33066a 81 .3 91 .7 0.014 80.8 91 .7 0.01 2 C At3g57540a 100 99.3 0.931 100 92.3 0.227

4 N150 At3g33066a 96 94.3 0.880 95.8 94.3 0.892 3 C At3g57540a 100 100 1.000 100 96 0.579

5 N150 At3g33066a 98 94.3 0.736 97.5 94.3 0.771 4 C At3g57540a 100 100 1.000 100 98 0.636

6 N150 At3g33066a 98 94.3 0.608 97.5 94.3 0.658 5 c At3g57540a 100 100 1.000 100 98 0.594

Gl N150 At3g33066a 0.35 0.38 0.288 0.35 0.38 0.226 6 c At3g57540a 100 100 1.000 100 98 0.58

1 N200 At3g33066a 0 0 1.000 0 0 1 Gl c At3g57540a 0.99 0.99 0.945 0.98 0.68 4E-07

2 N200 At3g33066a 0 0 1.000 0 0 1 1 A2.0 At3g57540a 3.67 2.67 0.886 1 1 1

3 N200 At3g33066a 0.67 1 0.935 0.79 1 0.96 2 A2.0 At3g57540a 79.3 6.67 0.000 22 7.67 0.026

4 N200 At3g33066a 14.3 28 0.218 14.3 28 0.218 3 A2.0 At3g57540a 94.3 20 0.000 95 39.3 1 E-10

5 N200 At3g33066a 33.3 62.3 0.009 33.3 62.3 0.009 4 A2.0 At3g57540a 96 52.3 0.000 96.3 82.7 0.002

6 N200 At3g33066a 54.3 76.3 0.003 54.3 76.3 0.003 5 A2.0 At3g57540a 96 93.3 0.31 1 97.3 85.3 0.002

Gl N200 At3g33066a 0.1 1 0.16 0.053 0.1 1 0.16 0.054 6 A2.0 At3g57540a 96 94.3 0.504 97.3 85.3 0.001

1 C At3g33066b 97.7 98 0.912 97.5 98 0.869 Gl A2.0 At3g57540a 0.47 0.26 0.000 0.36 0.26 0.056

2 c At3g33066b 98.3 98.7 0.945 98.3 98.7 0.946 1 C At1 g77450a 100 100 1.000 100 100 1

3 c At3g33066b 98.3 98.7 0.935 98.3 98.7 0.935 2 C At1 g77450a 100 100 1.000 100 100 1

4 c At3g33066b 99.3 98.7 0.952 99.2 98.7 0.964 3 C At1 g77450a 100 100 1.000 100 100 1

5 c At3g33066b 99.3 98.7 0.951 99.2 98.7 0.963 4 C At1 g77450a 100 100 1.000 100 100 1

6 c At3g33066b 99.3 98.7 0.926 99.2 98.7 0.944 5 C At1 g77450a 100 100 1.000 100 100 1

Gl c At3g33066b 0.98 0.98 0.951 0.98 0.98 1 1 HS90 At1 g77450a 100 100 1.000 100 100 1

1 M250 At3g33066b 9.33 14.3 0.101 9.25 14.3 0.097 2 HS90 At1 g77450a 100 100 1.000 89 55.3 0.003

2 M250 At3g33066b 88.3 95.7 0.135 88.2 95.7 0.127 3 HS90 At1 g77450a 96.3 87.3 0.373 45.5 9.5 3E-06

3 M250 At3g33066b 100 96.7 0.419 100 96.7 0.418 4 HS90 At1 g77450a 62.5 9.75 0.000 22.5 0.75 3E-04

4 M250 At3g33066b 100 97.3 0.809 100 97.3 0.81 5 HS90 At1 g77450a 61 7.75 0.000 22.5 0.75 7E-04

5 M250 At3g33066b 100 98.3 0.878 100 98.3 0.878 1 HS150 At1 g77450a 100 100 1.000 98 97.5 0.943

6 M250 At3g33066b 100 98.3 0.815 100 98.3 0.815 2 HS150 At1 g77450a 100 98.8 0.163 0 2 0.855

Gl M250 At3g33066b 0.53 0.56 0.251 0.53 0.56 0.275 3 HS150 At1 g77450a 13.5 0.75 0.208 0 0 1

1 M500 At3g33066b 0 0 1.000 0 0 1 4 HS150 At1 g77450a 2.75 0.75 0.866 0 0 1

2 M500 At3g33066b 0 0 1.000 0 0 1 5 HS150 At1 g77450a 1.5 0 0.896 0 0 1

3 M500 At3g33066b 1 3.33 0.571 0.85 3.33 0.546 1 C At4g23190a 100 100 1.000 100 100 1

Claims

1 . A method for increasing the tolerance to stress conditions of a plant, plant part, plant cell or seed or for increasing growth rate and/or biomass of a plant, plant part, plant cell or seed, comprising the step of modulating the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

2. The method according to claim 1 , wherein said modulating the expression and/or activity of said protein comprises expressing in said plant, plant part, plant cell or seed a chimeric gene comprising the following operably linked elements:

a. A plant-expressible promoter

b. A nucleic acid which when transcribed yields an RNA molecule that modulates the expression and/or activity of said protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64, SEQ ID NO. 66, SEQ ID NO. 68, SEQ ID NO. 70, SEQ ID NO. 72, SEQ ID NO. 74, SEQ ID NO. 76, SEQ ID NO. 78 or SEQ ID NO. 80, SEQ ID NO. 82, SEQ ID NO. 84, SEQ ID NO. 86, SEQ ID NO. 88, SEQ ID NO. 90.

c. Optionally, a 3' end region functional in plants

3. The method according to claim 1 or 2, wherein said modulating the expression and/or activity of a protein comprises decreasing the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

4. The method of claim 2 or 3, wherein said RNA molecule decreases the expression and/or activity of a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

5. The method of claim 4, wherein said RNA molecule comprises at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of any one of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

6. The method of claim 4, wherein said RNA molecule comprises at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of any one of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

7. The method of claim 4, wherein said RNA molecule comprises a sense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the nucleotide sequence of a gene present in said plant, plant part, plant cell or seed, said gene encoding a protein having the activity of a protein having the amino acid sequence of any one of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and an antisense region comprising a nucleotide sequence of at least 21 nucleotides having at least 76% sequence identity to the complement of the nucleotide sequence of said gene, wherein said sense and antisense region are capable of forming a double stranded RNA region comprising said at least 21 nucleotides.

8. The method of any one of claims 5-7, wherein said RNA region comprises at least 21 nucleotides having at least 76% sequence identity to a nucleotide sequence encoding a protein having at least 70% sequence identity to a protein having the amino acid sequence of any one of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64 and/or at least 21 nucleotides having at least 76% sequence identity to the complement of a nucleotide sequence having at least 70% sequence identity to any one of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

9. The method of any one of claims 5-8, wherein said RNA region comprises at least 21 nucleotides having at least 76% sequence identity to any one of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63, and/or at least 21 nucleotides having at least 76% sequence identity to the complement of any one of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33 , SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39, SEQ ID NO. 41 , SEQ ID NO. 43, SEQ ID NO. 45, SEQ ID NO. 47, SEQ ID NO. 49, SEQ ID NO. 51 , SEQ ID NO. 53, SEQ ID NO. 55, SEQ ID NO. 57, SEQ ID NO. 59, SEQ ID NO. 61 , SEQ ID NO. 63.

10. The method of claim 3, wherein said decreasing the expression and/or activity comprises introducing into said plant, plant part, plant cell or seed a knock-out allele of a gene encoding a protein having the activity of a protein having the amino acid sequence of SEQ ID NO. 2., SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 42, SEQ ID NO. 44, SEQ ID NO. 46, SEQ ID NO. 48, SEQ ID NO. 50, SEQ ID NO. 52, SEQ ID NO. 54, SEQ ID NO. 56, SEQ ID NO. 58, SEQ ID NO. 60, SEQ ID NO. 62, SEQ ID NO. 64.

1 1 . The method of any one of claims 1 -10, wherein said stress condition is selected from salt stress, osmotic stress, ABA treatment, heat stress, drought stress.

12. A chimeric gene as described in any one of claims 2-9.

13. A knock-out allele as described in claim 10.

14. A plant, plant part or plant cell comprising the chimeric gene of claim 12.

15. A plant, plant part or plant cell comprising the knock-out allele of claim 13.

16. Use of the chimeric gene of claim 12 or the mutant allele of claim 13 to produce a plant, plant part, plant cell or seed with increased stress tolerance and/or increased growth rate and/or biomass.