Limits...
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

Significant GO term associations in leaf developmental patterns. Gene Ontology (GO) terms that were significantly enriched in the identified gene expression profiles from developing leaves are shown. The number of genes included in each profile is shown in the box that represents the expression pattern of the included genes. A full listing of significant GO-terms can be found in Additional file 7
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Significant GO term associations in leaf developmental patterns. Gene Ontology (GO) terms that were significantly enriched in the identified gene expression profiles from developing leaves are shown. The number of genes included in each profile is shown in the box that represents the expression pattern of the included genes. A full listing of significant GO-terms can be found in Additional file 7

Mentions: To characterize the biochemical and physiological processes occurring during different stages of leaf development, we used Gene Ontology Term (GO-term) enrichment analysis [22] to identify groups of genes involved in similar functions that were significantly enriched within the co-regulated gene sets that were identified. A table listing all enriched GO-terms and associated genes identified in each leaf or cotyledon expression profile is given in Additional file 7, and summarized in Figs. 2 & 3. Genes belonging to profile 2 or 3 that decreased significantly between stage L-I and L-II or L-III fell into several classes, predominantly associated with cell growth and expansion, cell wall biosynthesis, cell wall thickening and loosening, as well as the development of the epidermal cell layer and cuticular wax biosynthesis (Fig. 2). This finding is consistent with the L-I stage being critical for leaf expansion and maturation (Leaves are fully expanded by stage L-II). Genes associated with photosynthetic processes and light response decreased in expression during the later stages of L-IV and L-V (profile 4) consistent with the decline of photosynthesis as the tissues began to senesce. Genes expressed at higher levels in the later stages (profile 10) function in arginine and glutamate transport, consistent with remobilization of amino acids (nitrogen) from the senescing tissues. Seven genes with predicted roles in sulfate assimilation are upregulated early (profile 7) which is consistent with the previously observed developmental regulation of the ATP sulfurylase genes [23]. A significant number of genes potentially involved in disease resistance and defense responses were also upregulated after stage L-III, which is consistent with the overlapping functions of many senescence-associated genes in responses to biotic stress (reviewed in [24]).Fig. 2


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

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

Significant GO term associations in leaf developmental patterns. Gene Ontology (GO) terms that were significantly enriched in the identified gene expression profiles from developing leaves are shown. The number of genes included in each profile is shown in the box that represents the expression pattern of the included genes. A full listing of significant GO-terms can be found in Additional file 7
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Significant GO term associations in leaf developmental patterns. Gene Ontology (GO) terms that were significantly enriched in the identified gene expression profiles from developing leaves are shown. The number of genes included in each profile is shown in the box that represents the expression pattern of the included genes. A full listing of significant GO-terms can be found in Additional file 7
Mentions: To characterize the biochemical and physiological processes occurring during different stages of leaf development, we used Gene Ontology Term (GO-term) enrichment analysis [22] to identify groups of genes involved in similar functions that were significantly enriched within the co-regulated gene sets that were identified. A table listing all enriched GO-terms and associated genes identified in each leaf or cotyledon expression profile is given in Additional file 7, and summarized in Figs. 2 & 3. Genes belonging to profile 2 or 3 that decreased significantly between stage L-I and L-II or L-III fell into several classes, predominantly associated with cell growth and expansion, cell wall biosynthesis, cell wall thickening and loosening, as well as the development of the epidermal cell layer and cuticular wax biosynthesis (Fig. 2). This finding is consistent with the L-I stage being critical for leaf expansion and maturation (Leaves are fully expanded by stage L-II). Genes associated with photosynthetic processes and light response decreased in expression during the later stages of L-IV and L-V (profile 4) consistent with the decline of photosynthesis as the tissues began to senesce. Genes expressed at higher levels in the later stages (profile 10) function in arginine and glutamate transport, consistent with remobilization of amino acids (nitrogen) from the senescing tissues. Seven genes with predicted roles in sulfate assimilation are upregulated early (profile 7) which is consistent with the previously observed developmental regulation of the ATP sulfurylase genes [23]. A significant number of genes potentially involved in disease resistance and defense responses were also upregulated after stage L-III, which is consistent with the overlapping functions of many senescence-associated genes in responses to biotic stress (reviewed in [24]).Fig. 2

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