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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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Differential expression of genes during short-day treatment.A. Number of genes significantly up-or down-regulated during the short-day treatment relative to the previous time point is indicated. B. K-means clustering illustrating the expression (Z-score normalized) profile of the soybean leaf and SAM transcriptome. Twenty clusters were used for a total of 15, 210 transcripts with significant expression profile changes in either leaf or SAM. Total number of transcripts in each cluster is indicated in parentheses. L0–L3: samples derived from leaf after 0-short-day (L0), 1-short-day (L1), 2-short-day (L2) or 3-short-day (L3) treatment. S0–S4: samples derived from SAM after 0-short-day (S0), 1-short-day (S1), 2-short-day (S2), 3-short-day (S3) or 4-short-day (S4) treatment.
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pone-0065319-g002: Differential expression of genes during short-day treatment.A. Number of genes significantly up-or down-regulated during the short-day treatment relative to the previous time point is indicated. B. K-means clustering illustrating the expression (Z-score normalized) profile of the soybean leaf and SAM transcriptome. Twenty clusters were used for a total of 15, 210 transcripts with significant expression profile changes in either leaf or SAM. Total number of transcripts in each cluster is indicated in parentheses. L0–L3: samples derived from leaf after 0-short-day (L0), 1-short-day (L1), 2-short-day (L2) or 3-short-day (L3) treatment. S0–S4: samples derived from SAM after 0-short-day (S0), 1-short-day (S1), 2-short-day (S2), 3-short-day (S3) or 4-short-day (S4) treatment.

Mentions: Among the 48,623 transcripts, 13,253 (27%) were expressed below 1 read per kb per million (RPKM) reads in all samples and these were excluded from further analysis since a further down-regulation or up-regulation to below 1 RPKM level may not have significant effect on the developmental switch under study. To identify genes differentially regulated by the exposure to short-day and hence floral initiation process through transcriptome sequencing, we compared expression levels at consecutive time points using Audic-Claverie statistics [18] with false discovery rate [21] controlled at 0.1%. We identified 2951 sequences that were differentially expressed in the SAM while 13,609 genes with significant profile changes were uncovered from the leaf samples (Figure 2A). The transition to short-day caused the most perturbation in leaf transcriptome especially following 1short-day treatment as 11,741 transcripts were differentially regulated at 1short-day in the leaf in comparison to that on 0short-day (Figure 2A); representing close to 92% of the total number of sequences with significant profile changes detected in the leaf. Similarly, in the SAM, most changes in mRNA level occurred after 1short-day treatment with a total of 1743 sequences significantly differentially regulated following by the S4-S3 with a total of 993 sequences (Figure 2A). The later is likely a result of major reprogramming occurring in the SAM necessary for the floral initiation to occur.


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

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

Differential expression of genes during short-day treatment.A. Number of genes significantly up-or down-regulated during the short-day treatment relative to the previous time point is indicated. B. K-means clustering illustrating the expression (Z-score normalized) profile of the soybean leaf and SAM transcriptome. Twenty clusters were used for a total of 15, 210 transcripts with significant expression profile changes in either leaf or SAM. Total number of transcripts in each cluster is indicated in parentheses. L0–L3: samples derived from leaf after 0-short-day (L0), 1-short-day (L1), 2-short-day (L2) or 3-short-day (L3) treatment. S0–S4: samples derived from SAM after 0-short-day (S0), 1-short-day (S1), 2-short-day (S2), 3-short-day (S3) or 4-short-day (S4) treatment.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3675103&req=5

pone-0065319-g002: Differential expression of genes during short-day treatment.A. Number of genes significantly up-or down-regulated during the short-day treatment relative to the previous time point is indicated. B. K-means clustering illustrating the expression (Z-score normalized) profile of the soybean leaf and SAM transcriptome. Twenty clusters were used for a total of 15, 210 transcripts with significant expression profile changes in either leaf or SAM. Total number of transcripts in each cluster is indicated in parentheses. L0–L3: samples derived from leaf after 0-short-day (L0), 1-short-day (L1), 2-short-day (L2) or 3-short-day (L3) treatment. S0–S4: samples derived from SAM after 0-short-day (S0), 1-short-day (S1), 2-short-day (S2), 3-short-day (S3) or 4-short-day (S4) treatment.
Mentions: Among the 48,623 transcripts, 13,253 (27%) were expressed below 1 read per kb per million (RPKM) reads in all samples and these were excluded from further analysis since a further down-regulation or up-regulation to below 1 RPKM level may not have significant effect on the developmental switch under study. To identify genes differentially regulated by the exposure to short-day and hence floral initiation process through transcriptome sequencing, we compared expression levels at consecutive time points using Audic-Claverie statistics [18] with false discovery rate [21] controlled at 0.1%. We identified 2951 sequences that were differentially expressed in the SAM while 13,609 genes with significant profile changes were uncovered from the leaf samples (Figure 2A). The transition to short-day caused the most perturbation in leaf transcriptome especially following 1short-day treatment as 11,741 transcripts were differentially regulated at 1short-day in the leaf in comparison to that on 0short-day (Figure 2A); representing close to 92% of the total number of sequences with significant profile changes detected in the leaf. Similarly, in the SAM, most changes in mRNA level occurred after 1short-day treatment with a total of 1743 sequences significantly differentially regulated following by the S4-S3 with a total of 993 sequences (Figure 2A). The later is likely a result of major reprogramming occurring in the SAM necessary for the floral initiation to occur.

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