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The dynamics of soybean leaf and shoot apical meristem transcriptome undergoing floral initiation process.

Wong CE, Singh MB, Bhalla PL - PLoS ONE (2013)

Bottom Line: A total of 2951 shoot apical meristem and 13,609 leaf sequences with significant profile changes during the time course examined were identified.Transcripts associated with protein degradation were also significantly changing in leaf and SAM implicating their involvement in triggering the developmental switch.Further, evidence is emerging that the conversion of shoot apical meristem to inflorescence meristem is linked with the interplay of auxin, cytokinin and GA creating a low cytokinin and high GA environment.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology and Biotechnology Group, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia.

ABSTRACT
Flowering process governs seed set and thus affects agricultural productivity. Soybean, a major legume crop, requires short-day photoperiod conditions for flowering. While leaf-derived signal(s) are essential for the photoperiod-induced floral initiation process at the shoot apical meristem, molecular events associated with early floral transition stages in either leaves or shoot apical meristems are not well understood. To provide novel insights into the molecular basis of floral initiation, RNA-Seq was used to characterize the soybean transcriptome of leaf and micro-dissected shoot apical meristem at different time points after short-day treatment. Shoot apical meristem expressed a higher number of transcripts in comparison to that of leaf highlighting greater diversity and abundance of transcripts expressed in the shoot apical meristem. A total of 2951 shoot apical meristem and 13,609 leaf sequences with significant profile changes during the time course examined were identified. Most changes in mRNA level occurred after 1short-day treatment. Transcripts involved in mediating responses to stimulus including hormones or in various metabolic processes represent the top enriched GO functional category for the SAM and leaf dataset, respectively. Transcripts associated with protein degradation were also significantly changing in leaf and SAM implicating their involvement in triggering the developmental switch. RNA-Seq analysis of shoot apical meristem and leaf from soybean undergoing floral transition reveal major reprogramming events in leaves and the SAM that point toward hormones gibberellins (GA) and cytokinin as key regulators in the production of systemic flowering signal(s) in leaves. These hormones may form part of the systemic signals in addition to the established florigen, FLOWERING LOCUS T (FT). Further, evidence is emerging that the conversion of shoot apical meristem to inflorescence meristem is linked with the interplay of auxin, cytokinin and GA creating a low cytokinin and high GA environment.

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Expression of putative ethylene and ABA biosynthesis and signaling genes in soybean.A. A schematic diagram depicting ethylene biosynthesis and signaling [69] is given on the left while expression data of differentially expressed transcripts for respective annotated homologs are given on the right panel. Ethylene is perceived by repressing the action of receptor complexes including ETR/ERS/EIN4 receptors, RTE1, and Raf-like protein kinase CTR1, which negatively regulates downstream signaling component. When EIN2 is activated in the presence of ethylene, it stabilizes EIN3. EIN5/XRN4 regulates EBF1 (EIN3 BINDING F-BOX1) that degrades EIN3 in the absence of ethylene. B. Expression data of differentially expressed transcripts related to ABA (top) or trehalose (bottom) metabolism are shown. NCED, Nine-cis-epoxycarotenoid dioxygenase; AAO3, abscisic aldehyde oxidase3; UGT84B1, ABA glucosyltransferase; CYP707A, ABA hydroxylase; GPCR, G-protein coupled receptor for ABA; ABA4, ABA-deficient 4; ABF1, ABA-responsive element-binding factor1. Expression level is as in Figure 3.
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pone-0065319-g004: Expression of putative ethylene and ABA biosynthesis and signaling genes in soybean.A. A schematic diagram depicting ethylene biosynthesis and signaling [69] is given on the left while expression data of differentially expressed transcripts for respective annotated homologs are given on the right panel. Ethylene is perceived by repressing the action of receptor complexes including ETR/ERS/EIN4 receptors, RTE1, and Raf-like protein kinase CTR1, which negatively regulates downstream signaling component. When EIN2 is activated in the presence of ethylene, it stabilizes EIN3. EIN5/XRN4 regulates EBF1 (EIN3 BINDING F-BOX1) that degrades EIN3 in the absence of ethylene. B. Expression data of differentially expressed transcripts related to ABA (top) or trehalose (bottom) metabolism are shown. NCED, Nine-cis-epoxycarotenoid dioxygenase; AAO3, abscisic aldehyde oxidase3; UGT84B1, ABA glucosyltransferase; CYP707A, ABA hydroxylase; GPCR, G-protein coupled receptor for ABA; ABA4, ABA-deficient 4; ABF1, ABA-responsive element-binding factor1. Expression level is as in Figure 3.

Mentions: Ethylene biosynthetic transcripts as well as key signaling components are specifically enriched in the leaf dataset and these range from membrane receptors to protein kinases (Figure 4A). A great majority of these (49 out of 61) was up-regulated following 1short-day treatment while some at a later time point on 3short-day with one putative ETHYLENE RESPONSE FACTOR1 (ERF1, Glyma10g04210.1) displaying the highest fold of increase (48-fold) on 1 short-day in comparison to 0 short-day. Ethylene has been long regarded as a growth inhibitor as well as a key coordinator of stress responses. The observation that many transcripts involved in coordinating cell expansion and cell division were down-regulated while stress-related sequences were up-regulated on 1-short-day in the leaf (Table S1) implicates ethylene having a role in regulating their expression. For instance, the growth arrest may be regulated by positive ethylene signaling since ethylene is known to inhibit growth in a DELLA-dependent manner [36] and there were markedly increased expression of these growth repressors (Glyma08g10140.1, Glyma05g27190.1, Glyma05g27190.1) in the leaf following 1short-day (Figure 5). The possible increase of ABA level in the leaf as indicated by the up-regulation of a number of ABA biosynthetic transcripts (Figure 4B) could also play similar roles in inhibiting growth and up-regulating stress-responsive transcripts (Table S1). Strikingly, there is also an increased expression of transcripts that break down ABA in the leaf dataset (Figure 4B) implying an autoregulatory mode for the maintenance of hormone homeostasis.


The dynamics of soybean leaf and shoot apical meristem transcriptome undergoing floral initiation process.

Wong CE, Singh MB, Bhalla PL - PLoS ONE (2013)

Expression of putative ethylene and ABA biosynthesis and signaling genes in soybean.A. A schematic diagram depicting ethylene biosynthesis and signaling [69] is given on the left while expression data of differentially expressed transcripts for respective annotated homologs are given on the right panel. Ethylene is perceived by repressing the action of receptor complexes including ETR/ERS/EIN4 receptors, RTE1, and Raf-like protein kinase CTR1, which negatively regulates downstream signaling component. When EIN2 is activated in the presence of ethylene, it stabilizes EIN3. EIN5/XRN4 regulates EBF1 (EIN3 BINDING F-BOX1) that degrades EIN3 in the absence of ethylene. B. Expression data of differentially expressed transcripts related to ABA (top) or trehalose (bottom) metabolism are shown. NCED, Nine-cis-epoxycarotenoid dioxygenase; AAO3, abscisic aldehyde oxidase3; UGT84B1, ABA glucosyltransferase; CYP707A, ABA hydroxylase; GPCR, G-protein coupled receptor for ABA; ABA4, ABA-deficient 4; ABF1, ABA-responsive element-binding factor1. Expression level is as in Figure 3.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3675103&req=5

pone-0065319-g004: Expression of putative ethylene and ABA biosynthesis and signaling genes in soybean.A. A schematic diagram depicting ethylene biosynthesis and signaling [69] is given on the left while expression data of differentially expressed transcripts for respective annotated homologs are given on the right panel. Ethylene is perceived by repressing the action of receptor complexes including ETR/ERS/EIN4 receptors, RTE1, and Raf-like protein kinase CTR1, which negatively regulates downstream signaling component. When EIN2 is activated in the presence of ethylene, it stabilizes EIN3. EIN5/XRN4 regulates EBF1 (EIN3 BINDING F-BOX1) that degrades EIN3 in the absence of ethylene. B. Expression data of differentially expressed transcripts related to ABA (top) or trehalose (bottom) metabolism are shown. NCED, Nine-cis-epoxycarotenoid dioxygenase; AAO3, abscisic aldehyde oxidase3; UGT84B1, ABA glucosyltransferase; CYP707A, ABA hydroxylase; GPCR, G-protein coupled receptor for ABA; ABA4, ABA-deficient 4; ABF1, ABA-responsive element-binding factor1. Expression level is as in Figure 3.
Mentions: Ethylene biosynthetic transcripts as well as key signaling components are specifically enriched in the leaf dataset and these range from membrane receptors to protein kinases (Figure 4A). A great majority of these (49 out of 61) was up-regulated following 1short-day treatment while some at a later time point on 3short-day with one putative ETHYLENE RESPONSE FACTOR1 (ERF1, Glyma10g04210.1) displaying the highest fold of increase (48-fold) on 1 short-day in comparison to 0 short-day. Ethylene has been long regarded as a growth inhibitor as well as a key coordinator of stress responses. The observation that many transcripts involved in coordinating cell expansion and cell division were down-regulated while stress-related sequences were up-regulated on 1-short-day in the leaf (Table S1) implicates ethylene having a role in regulating their expression. For instance, the growth arrest may be regulated by positive ethylene signaling since ethylene is known to inhibit growth in a DELLA-dependent manner [36] and there were markedly increased expression of these growth repressors (Glyma08g10140.1, Glyma05g27190.1, Glyma05g27190.1) in the leaf following 1short-day (Figure 5). The possible increase of ABA level in the leaf as indicated by the up-regulation of a number of ABA biosynthetic transcripts (Figure 4B) could also play similar roles in inhibiting growth and up-regulating stress-responsive transcripts (Table S1). Strikingly, there is also an increased expression of transcripts that break down ABA in the leaf dataset (Figure 4B) implying an autoregulatory mode for the maintenance of hormone homeostasis.

Bottom Line: A total of 2951 shoot apical meristem and 13,609 leaf sequences with significant profile changes during the time course examined were identified.Transcripts associated with protein degradation were also significantly changing in leaf and SAM implicating their involvement in triggering the developmental switch.Further, evidence is emerging that the conversion of shoot apical meristem to inflorescence meristem is linked with the interplay of auxin, cytokinin and GA creating a low cytokinin and high GA environment.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology and Biotechnology Group, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia.

ABSTRACT
Flowering process governs seed set and thus affects agricultural productivity. Soybean, a major legume crop, requires short-day photoperiod conditions for flowering. While leaf-derived signal(s) are essential for the photoperiod-induced floral initiation process at the shoot apical meristem, molecular events associated with early floral transition stages in either leaves or shoot apical meristems are not well understood. To provide novel insights into the molecular basis of floral initiation, RNA-Seq was used to characterize the soybean transcriptome of leaf and micro-dissected shoot apical meristem at different time points after short-day treatment. Shoot apical meristem expressed a higher number of transcripts in comparison to that of leaf highlighting greater diversity and abundance of transcripts expressed in the shoot apical meristem. A total of 2951 shoot apical meristem and 13,609 leaf sequences with significant profile changes during the time course examined were identified. Most changes in mRNA level occurred after 1short-day treatment. Transcripts involved in mediating responses to stimulus including hormones or in various metabolic processes represent the top enriched GO functional category for the SAM and leaf dataset, respectively. Transcripts associated with protein degradation were also significantly changing in leaf and SAM implicating their involvement in triggering the developmental switch. RNA-Seq analysis of shoot apical meristem and leaf from soybean undergoing floral transition reveal major reprogramming events in leaves and the SAM that point toward hormones gibberellins (GA) and cytokinin as key regulators in the production of systemic flowering signal(s) in leaves. These hormones may form part of the systemic signals in addition to the established florigen, FLOWERING LOCUS T (FT). Further, evidence is emerging that the conversion of shoot apical meristem to inflorescence meristem is linked with the interplay of auxin, cytokinin and GA creating a low cytokinin and high GA environment.

Show MeSH
Related in: MedlinePlus