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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

Specific families of leaf transcription factors are enriched in early leaf development and senescence phases. Differentially expressed transcription factors categorized by expression profile and classified by family. Transcription factor families represented by more than twenty genes are shown [31]
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Fig6: Specific families of leaf transcription factors are enriched in early leaf development and senescence phases. Differentially expressed transcription factors categorized by expression profile and classified by family. Transcription factor families represented by more than twenty genes are shown [31]

Mentions: The transcription factors from both the cotyledon and leaves were placed into bins based on annotated family [31]. We found representatives of 60 different families of transcription factors in the cotyledon and 57 families in the leaf. The most abundant transcription factor families (containing 20 or more genes) are shown in Fig. 6 for leaves and Fig. 7 for cotyledons. In both tissues, we observe that the transcription factors most commonly found to increase in expression with tissue age are from the WRKY family and these comprise the largest family of transcriptional regulators expressed differentially in our dataset. This is consistent with previous studies that find these transcription factors to function as major regulators of senescence [29, 32–34]. Additionally, members of the GRAS family are also expressed predominantly during leaf senescence and early cotyledon senescence, consistent with studies in other species [35–37]. Twenty-one of the GRAS transcription factors were upregulated during senescence in both cotyledons and leaves. In leaves, the bHLH, C2C2(DOF) zinc finger transcription factors, and G2-like transcription factors share the expression profiles (profiles 2–4) that span the photosynthetic period, consistent with a likely role in chloroplast development and regulation of photosynthetic genes and carbohydrate metabolism [38–41]. Auxin plays an important role in plant growth and development by regulating gene expression [42]. In both the leaf and cotyledon, the Aux/IAA transcription factors decrease in expression following the initial stages of development (leaf profile 3 and cotyledon profile 2). This result is consistent with studies of senescence in cotton, rice, and wheat suggesting these transcription factors may act as negative regulators of senescence [43–45]. Of 7,251 genes identified by MapMan as transcription factors, only six were annotated as part of the NAC family. As these transcription factors are known to be involved in senescence and defense [14, 21, 46], we examined the Gmax_189 genome annotations to identify 236 NAC or NAC-related transcription factors (Additional file 11), 38 of these were found to differentially expressed in the leaves and 54 in the cotyledon. The majority of the differentially expressed NAC transcription factors (23 in leaf and 40 in cotyledon) were upregulated during tissue senescence, with 8 genes common to both organs.Fig. 6


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

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

Specific families of leaf transcription factors are enriched in early leaf development and senescence phases. Differentially expressed transcription factors categorized by expression profile and classified by family. Transcription factor families represented by more than twenty genes are shown [31]
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Specific families of leaf transcription factors are enriched in early leaf development and senescence phases. Differentially expressed transcription factors categorized by expression profile and classified by family. Transcription factor families represented by more than twenty genes are shown [31]
Mentions: The transcription factors from both the cotyledon and leaves were placed into bins based on annotated family [31]. We found representatives of 60 different families of transcription factors in the cotyledon and 57 families in the leaf. The most abundant transcription factor families (containing 20 or more genes) are shown in Fig. 6 for leaves and Fig. 7 for cotyledons. In both tissues, we observe that the transcription factors most commonly found to increase in expression with tissue age are from the WRKY family and these comprise the largest family of transcriptional regulators expressed differentially in our dataset. This is consistent with previous studies that find these transcription factors to function as major regulators of senescence [29, 32–34]. Additionally, members of the GRAS family are also expressed predominantly during leaf senescence and early cotyledon senescence, consistent with studies in other species [35–37]. Twenty-one of the GRAS transcription factors were upregulated during senescence in both cotyledons and leaves. In leaves, the bHLH, C2C2(DOF) zinc finger transcription factors, and G2-like transcription factors share the expression profiles (profiles 2–4) that span the photosynthetic period, consistent with a likely role in chloroplast development and regulation of photosynthetic genes and carbohydrate metabolism [38–41]. Auxin plays an important role in plant growth and development by regulating gene expression [42]. In both the leaf and cotyledon, the Aux/IAA transcription factors decrease in expression following the initial stages of development (leaf profile 3 and cotyledon profile 2). This result is consistent with studies of senescence in cotton, rice, and wheat suggesting these transcription factors may act as negative regulators of senescence [43–45]. Of 7,251 genes identified by MapMan as transcription factors, only six were annotated as part of the NAC family. As these transcription factors are known to be involved in senescence and defense [14, 21, 46], we examined the Gmax_189 genome annotations to identify 236 NAC or NAC-related transcription factors (Additional file 11), 38 of these were found to differentially expressed in the leaves and 54 in the cotyledon. The majority of the differentially expressed NAC transcription factors (23 in leaf and 40 in cotyledon) were upregulated during tissue senescence, with 8 genes common to both organs.Fig. 6

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