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An RNA-Seq based gene expression atlas of the common bean.

O'Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP - BMC Genomics (2014)

Bottom Line: Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization.These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen.Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St, Paul, MN 55108, USA. jamie.orourke@ars.usda.gov.

ABSTRACT

Background: Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species.

Results: Combining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form.

Conclusions: These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

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Related in: MedlinePlus

Seed master transcription factor expression. The expression profiles (as Z-scores: red = high, blue = low) of four transcription factors that regulate seed development in multiple species. Note the low expression of LEC2 (RPKM = 4) and WRI1 (RPKM = 5–9) in developing seeds. See Table 1 for tissue descriptions.
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Fig4: Seed master transcription factor expression. The expression profiles (as Z-scores: red = high, blue = low) of four transcription factors that regulate seed development in multiple species. Note the low expression of LEC2 (RPKM = 4) and WRI1 (RPKM = 5–9) in developing seeds. See Table 1 for tissue descriptions.

Mentions: Seed development in multiple species is regulated by four master TFs: LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and WRINKLED 1 (WRI1)[21, 22, 30]. Using BLASTP, we queried the Arabidopsis protein sequences to identify homologous sequences in the Pv predicted genes (Figure 4). The homolog for LEC2 was only weakly expressed (RPKM = 4) mid-seed development in Pv. Seeds of Arabidopsis loss of function lec2 mutants accumulated 15% less protein and 30% less oil while the seed starch content increased five fold as compared to wild type plants [31]. The altered seed composition of lec2 mutant plants closely resembles that of Pv, suggesting down regulation of LEC2 may affect seed composition. LEC2 controls the gene expression of WRI1, which also exhibits low expression patterns in Pv developing seeds (RPKM: SH = 5, S1 = 9, S2 = 5). WRI1 expression modulates the expression of a set of genes controlling late glycolysis and fatty acid biosynthesis. The low expression of both LEC2 and WRI1 may relate to the lower oil composition of Pv.Figure 4


An RNA-Seq based gene expression atlas of the common bean.

O'Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP - BMC Genomics (2014)

Seed master transcription factor expression. The expression profiles (as Z-scores: red = high, blue = low) of four transcription factors that regulate seed development in multiple species. Note the low expression of LEC2 (RPKM = 4) and WRI1 (RPKM = 5–9) in developing seeds. See Table 1 for tissue descriptions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4195886&req=5

Fig4: Seed master transcription factor expression. The expression profiles (as Z-scores: red = high, blue = low) of four transcription factors that regulate seed development in multiple species. Note the low expression of LEC2 (RPKM = 4) and WRI1 (RPKM = 5–9) in developing seeds. See Table 1 for tissue descriptions.
Mentions: Seed development in multiple species is regulated by four master TFs: LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and WRINKLED 1 (WRI1)[21, 22, 30]. Using BLASTP, we queried the Arabidopsis protein sequences to identify homologous sequences in the Pv predicted genes (Figure 4). The homolog for LEC2 was only weakly expressed (RPKM = 4) mid-seed development in Pv. Seeds of Arabidopsis loss of function lec2 mutants accumulated 15% less protein and 30% less oil while the seed starch content increased five fold as compared to wild type plants [31]. The altered seed composition of lec2 mutant plants closely resembles that of Pv, suggesting down regulation of LEC2 may affect seed composition. LEC2 controls the gene expression of WRI1, which also exhibits low expression patterns in Pv developing seeds (RPKM: SH = 5, S1 = 9, S2 = 5). WRI1 expression modulates the expression of a set of genes controlling late glycolysis and fatty acid biosynthesis. The low expression of both LEC2 and WRI1 may relate to the lower oil composition of Pv.Figure 4

Bottom Line: Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization.These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen.Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St, Paul, MN 55108, USA. jamie.orourke@ars.usda.gov.

ABSTRACT

Background: Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species.

Results: Combining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form.

Conclusions: These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.

Show MeSH
Related in: MedlinePlus