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Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

Brown AV, Hudson KA - BMC Plant Biol. (2015)

Bottom Line: Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development.The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets.These results help validate functional annotation for soybean genes and promoters.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. brown637@purdue.edu.

ABSTRACT

Background: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon.

Results: To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence.

Conclusions: The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed gene profiles in leaf and cotyledon development. Differentially expressed genes from (a) leaves and (b) cotyledons were classified into expression profiles based on significant changes in gene expression between subsequent stages. Line thickness is proportional to the number of genes included in each profile. See Methods for more detail
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Fig1: Differentially expressed gene profiles in leaf and cotyledon development. Differentially expressed genes from (a) leaves and (b) cotyledons were classified into expression profiles based on significant changes in gene expression between subsequent stages. Line thickness is proportional to the number of genes included in each profile. See Methods for more detail

Mentions: Of the 54,175 genes in the soybean Gmax189 dataset, 12,497 genes (23.1 %) were found to be differentially expressed between at least two stages within the cotyledon timecourse while 9,500 genes (17.5 %) were differentially expressed between two stages of the leaf timecourse. Each differentially expressed gene was assigned to an expression profile based on significant fold change and expression across all of the stages in an organ order to identify major dynamic patterns of gene expression (Fig. 1). Overall, the set of differentially expressed genes through cotyledon and leaf development agree well with results of prior studies of leaf senescence in Arabidopsis thaliana and other plants. Close homologs for thirty-one percent (31 %) of genes identified as SAGs in Arabidopsis [13] were found to be differentially expressed in the leaf dataset, while 44 % were differentially expressed in the cotyledon dataset (Additional file 6). For example, Arabidopsis gene AtNAP (At1g69490) is a NAC transcription factor that has an important role in leaf senescence [21]. The top soybean orthologs of this gene are Glyma13g35550, Glyma1g06150, Glyma20g04400, Glyma02g12220, and Glyma07g35630. All of these were found to be significantly upregulated in either cotyledon or leaf in this experiment suggesting conservation of function of this transcription factor in soybean leaf senescence.Fig. 1


Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

Brown AV, Hudson KA - BMC Plant Biol. (2015)

Differentially expressed gene profiles in leaf and cotyledon development. Differentially expressed genes from (a) leaves and (b) cotyledons were classified into expression profiles based on significant changes in gene expression between subsequent stages. Line thickness is proportional to the number of genes included in each profile. See Methods for more detail
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492100&req=5

Fig1: Differentially expressed gene profiles in leaf and cotyledon development. Differentially expressed genes from (a) leaves and (b) cotyledons were classified into expression profiles based on significant changes in gene expression between subsequent stages. Line thickness is proportional to the number of genes included in each profile. See Methods for more detail
Mentions: Of the 54,175 genes in the soybean Gmax189 dataset, 12,497 genes (23.1 %) were found to be differentially expressed between at least two stages within the cotyledon timecourse while 9,500 genes (17.5 %) were differentially expressed between two stages of the leaf timecourse. Each differentially expressed gene was assigned to an expression profile based on significant fold change and expression across all of the stages in an organ order to identify major dynamic patterns of gene expression (Fig. 1). Overall, the set of differentially expressed genes through cotyledon and leaf development agree well with results of prior studies of leaf senescence in Arabidopsis thaliana and other plants. Close homologs for thirty-one percent (31 %) of genes identified as SAGs in Arabidopsis [13] were found to be differentially expressed in the leaf dataset, while 44 % were differentially expressed in the cotyledon dataset (Additional file 6). For example, Arabidopsis gene AtNAP (At1g69490) is a NAC transcription factor that has an important role in leaf senescence [21]. The top soybean orthologs of this gene are Glyma13g35550, Glyma1g06150, Glyma20g04400, Glyma02g12220, and Glyma07g35630. All of these were found to be significantly upregulated in either cotyledon or leaf in this experiment suggesting conservation of function of this transcription factor in soybean leaf senescence.Fig. 1

Bottom Line: Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development.The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets.These results help validate functional annotation for soybean genes and promoters.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. brown637@purdue.edu.

ABSTRACT

Background: Immediately following germination, the developing soybean seedling relies on the nutrient reserves stored in the cotyledons to sustain heterotrophic growth. During the seed filling period, developing seeds rely on the transport of nutrients from the trifoliate leaves. In soybean, both cotyledons and leaves develop the capacity for photosynthesis, and subsequently senesce and abscise once their function has ended. Before this occurs, the nutrients they contain are mobilized and transported to other parts of the plant. These processes are carefully orchestrated by genetic regulation throughout the development of the leaf or cotyledon.

Results: To identify genes involved in the processes of leaf or cotyledon development and senescence in soybean, we used RNA-seq to profile multiple stages of cotyledon and leaf tissues. Differentially expressed genes between stages of leaf or cotyledon development were determined, major patterns of gene expression were defined, and shared genes were identified. Over 38,000 transcripts were expressed during the course of leaf and cotyledon development. Of those transcripts, 5,000 were expressed in a tissue specific pattern. Of the genes that were differentially expressed between both later stage tissues, 90 % had the same direction of change, suggesting that the mechanisms of senescence are conserved between tissues. Analysis of the enrichment of biological functions within genes sharing common expression profiles highlights the main processes occurring within these defined temporal windows of leaf and cotyledon development. Over 1,000 genes were identified with predicted regulatory functions that may have a role in control of leaf or cotyledon senescence.

Conclusions: The process of leaf and cotyledon development can be divided into distinct stages characterized by the expression of specific gene sets. The importance of the WRKY, NAC, and GRAS family transcription factors as major regulators of plant senescence is confirmed for both soybean leaf and cotyledon tissues. These results help validate functional annotation for soybean genes and promoters.

No MeSH data available.


Related in: MedlinePlus