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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

Significantly over-represented motifs in promoters of genes that change in expression during cotyledon senescence. The table shows the most significant promoter motifs (e-value cutoff less than e-05) and the number of occurrences (in italics) for each significant element found in promoters of genes classified in one of the eight expression profiles identified for differentially expressed cotyledon genes [47]. Where gene sets were too large for analysis, the top 425 or 450 genes (based on magnitude of fold change) were analyzed
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Fig9: Significantly over-represented motifs in promoters of genes that change in expression during cotyledon senescence. The table shows the most significant promoter motifs (e-value cutoff less than e-05) and the number of occurrences (in italics) for each significant element found in promoters of genes classified in one of the eight expression profiles identified for differentially expressed cotyledon genes [47]. Where gene sets were too large for analysis, the top 425 or 450 genes (based on magnitude of fold change) were analyzed

Mentions: To identify potential cis-acting elements that govern the temporal patterns of expression, over-represented promoter motifs were identified from genes in each profile using Elefinder [47, 48]. The Elefinder method identifies statistically over-represented, characterized binding sites for known transcription factors from a variety of plant species within a specified promoter set. This can suggest a likely mechanism for the control of the specific expression pattern of a gene although the incidence of a given binding site only suggests which class of transcription factor could recognize and regulate the promoter. Where gene sets were too large to scan for over-represented elements in their entirety, the top 400,425 or 450 genes (based on largest fold change) were analyzed. Fig. 8 lists all of the significant motifs associated with each expression pattern in leaves, and the associated e-value, and the number of occurrences of the element in the data set. In the leaf, elements present in the promoters of genes that decline from stage L-I throughout the timecourse (leaf profiles 1–4) are associated with photosynthetic genes, including the MYC2 binding site, the Ibox, and ATB2/AtbZIP44/AtbZIP53/GBF5 binding site. Similarly, genes included in cotyledon profiles 1 and 4 that decreased in expression between stages C-II and C-III contained the G-box and SORLIP1 element in their promoters, consistent with the known abundance of these motifs upstream of light regulated genes associated with photosynthesis. Photosynthesis genes were observed to be downregulated between these stages (Fig. 8), thus activation via these elements may be reduced during the studied period [47, 49, 50]. The ABFs element is enriched in promoters of genes declining in expression throughout the cotyledon timecourse, and is a G-box variant implicated in ABA response and targeted by bZIP transcription factors [51] (Fig. 9). The ARF1 binding site, targeted by the Aux/IAA transcription factors is enriched in genes downregulated in later stages of development in both the leaf (profiles 3 and 4) and cotyledon (profile 3) [52, 53]. In both leaves and cotyledons, the DPBF1&2 element is enriched in genes upregulated in later stages (for example, profiles 9 and 10 in the leaf and 5, 7, and 8 in the cotyledon) [54–56]. In both leaves and cotyledons, the AtHB6 motif is over-represented in genes that had a constant increase in expression (cotyledon profile 8 and leaf profile 10). The ATHB6 transcription factor is a member of the homeodomain-leucine zipper family of transcription factors thought to regulate active cell growth and differentiation (reviewed in [57]). The Bellringer/replumless/pennywise binding site is enriched in promoters of genes from multiple distinct expression profiles in cotyledons and leaves. This AT-rich cis-regulatory element is a target for homeodomain transcription factors, however in the context of regulation of the AGAMOUS gene in Arabidopsis the element is located within an intron [58]. In both tissues the WRKY-targeted W-box [14, 59] is the most significantly enriched promoter element, and occurs in genes that increase in expression leading up to leaf senescence.Fig. 8


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

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

Significantly over-represented motifs in promoters of genes that change in expression during cotyledon senescence. The table shows the most significant promoter motifs (e-value cutoff less than e-05) and the number of occurrences (in italics) for each significant element found in promoters of genes classified in one of the eight expression profiles identified for differentially expressed cotyledon genes [47]. Where gene sets were too large for analysis, the top 425 or 450 genes (based on magnitude of fold change) were analyzed
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig9: Significantly over-represented motifs in promoters of genes that change in expression during cotyledon senescence. The table shows the most significant promoter motifs (e-value cutoff less than e-05) and the number of occurrences (in italics) for each significant element found in promoters of genes classified in one of the eight expression profiles identified for differentially expressed cotyledon genes [47]. Where gene sets were too large for analysis, the top 425 or 450 genes (based on magnitude of fold change) were analyzed
Mentions: To identify potential cis-acting elements that govern the temporal patterns of expression, over-represented promoter motifs were identified from genes in each profile using Elefinder [47, 48]. The Elefinder method identifies statistically over-represented, characterized binding sites for known transcription factors from a variety of plant species within a specified promoter set. This can suggest a likely mechanism for the control of the specific expression pattern of a gene although the incidence of a given binding site only suggests which class of transcription factor could recognize and regulate the promoter. Where gene sets were too large to scan for over-represented elements in their entirety, the top 400,425 or 450 genes (based on largest fold change) were analyzed. Fig. 8 lists all of the significant motifs associated with each expression pattern in leaves, and the associated e-value, and the number of occurrences of the element in the data set. In the leaf, elements present in the promoters of genes that decline from stage L-I throughout the timecourse (leaf profiles 1–4) are associated with photosynthetic genes, including the MYC2 binding site, the Ibox, and ATB2/AtbZIP44/AtbZIP53/GBF5 binding site. Similarly, genes included in cotyledon profiles 1 and 4 that decreased in expression between stages C-II and C-III contained the G-box and SORLIP1 element in their promoters, consistent with the known abundance of these motifs upstream of light regulated genes associated with photosynthesis. Photosynthesis genes were observed to be downregulated between these stages (Fig. 8), thus activation via these elements may be reduced during the studied period [47, 49, 50]. The ABFs element is enriched in promoters of genes declining in expression throughout the cotyledon timecourse, and is a G-box variant implicated in ABA response and targeted by bZIP transcription factors [51] (Fig. 9). The ARF1 binding site, targeted by the Aux/IAA transcription factors is enriched in genes downregulated in later stages of development in both the leaf (profiles 3 and 4) and cotyledon (profile 3) [52, 53]. In both leaves and cotyledons, the DPBF1&2 element is enriched in genes upregulated in later stages (for example, profiles 9 and 10 in the leaf and 5, 7, and 8 in the cotyledon) [54–56]. In both leaves and cotyledons, the AtHB6 motif is over-represented in genes that had a constant increase in expression (cotyledon profile 8 and leaf profile 10). The ATHB6 transcription factor is a member of the homeodomain-leucine zipper family of transcription factors thought to regulate active cell growth and differentiation (reviewed in [57]). The Bellringer/replumless/pennywise binding site is enriched in promoters of genes from multiple distinct expression profiles in cotyledons and leaves. This AT-rich cis-regulatory element is a target for homeodomain transcription factors, however in the context of regulation of the AGAMOUS gene in Arabidopsis the element is located within an intron [58]. In both tissues the WRKY-targeted W-box [14, 59] is the most significantly enriched promoter element, and occurs in genes that increase in expression leading up to leaf senescence.Fig. 8

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