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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

Leaf and cotyledon specific genes. Of the 41,106 genes identified as expressed in the experiment, 7.4 % of genes were expressed exclusively in the cotyledons, 5 % of the genes were expressed only in the leaf, and more than 87 % were shared between the two tissues. The list complete list of genes that demonstrated tissue specific expression is included in Additional file 9
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Fig5: Leaf and cotyledon specific genes. Of the 41,106 genes identified as expressed in the experiment, 7.4 % of genes were expressed exclusively in the cotyledons, 5 % of the genes were expressed only in the leaf, and more than 87 % were shared between the two tissues. The list complete list of genes that demonstrated tissue specific expression is included in Additional file 9

Mentions: We determined that 36,012 transcripts (87.6 %) were expressed in both the cotyledon and the leaf, while the remainder of the genes showed evidence for specificity to either leaves or cotyledons in this experiment (Additional file 9). A total of 3,027 (7.4 %) genes were only present in cotyledons and 2,067 genes (5.0 %) were only expressed in the leaf (Fig. 5). Over-represented GO-terms associated with the cotyledon-specific genes suggest the mobilization of cotyledon-specific nutrients, including the response to trehalose stimulus and alpha-glucan/water dikinase activity. The chloroplast protein alpha-glucan water dikinase 1 mediates the incorporation of phosphate into starch-like alpha-glucan, mostly at the C-6 position of glucose units in Arabidopsis. This acts as an overall regulator of starch mobilization, and is required for starch degradation [28]. The β-amylase enzymes are involved in the hydrolysis of starch and an important step in germinating seedlings, and post germination growth [29, 30]. Over-represented functions for the leaf-specific genes include categories associated with photoperiodism and flower development, consistent with these processes occurring long after the cotyledons have senesced.Fig. 5


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

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

Leaf and cotyledon specific genes. Of the 41,106 genes identified as expressed in the experiment, 7.4 % of genes were expressed exclusively in the cotyledons, 5 % of the genes were expressed only in the leaf, and more than 87 % were shared between the two tissues. The list complete list of genes that demonstrated tissue specific expression is included in Additional file 9
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Leaf and cotyledon specific genes. Of the 41,106 genes identified as expressed in the experiment, 7.4 % of genes were expressed exclusively in the cotyledons, 5 % of the genes were expressed only in the leaf, and more than 87 % were shared between the two tissues. The list complete list of genes that demonstrated tissue specific expression is included in Additional file 9
Mentions: We determined that 36,012 transcripts (87.6 %) were expressed in both the cotyledon and the leaf, while the remainder of the genes showed evidence for specificity to either leaves or cotyledons in this experiment (Additional file 9). A total of 3,027 (7.4 %) genes were only present in cotyledons and 2,067 genes (5.0 %) were only expressed in the leaf (Fig. 5). Over-represented GO-terms associated with the cotyledon-specific genes suggest the mobilization of cotyledon-specific nutrients, including the response to trehalose stimulus and alpha-glucan/water dikinase activity. The chloroplast protein alpha-glucan water dikinase 1 mediates the incorporation of phosphate into starch-like alpha-glucan, mostly at the C-6 position of glucose units in Arabidopsis. This acts as an overall regulator of starch mobilization, and is required for starch degradation [28]. The β-amylase enzymes are involved in the hydrolysis of starch and an important step in germinating seedlings, and post germination growth [29, 30]. Over-represented functions for the leaf-specific genes include categories associated with photoperiodism and flower development, consistent with these processes occurring long after the cotyledons have senesced.Fig. 5

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