Dataset Information

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

ABSTRACT: The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in the SAM of the crop legume, soybean (Glycine max). A total of 331 transcripts displayed significant changes in their expression profiles. The in silico and RT-PCR analysis on differentially regulated transcripts implies the intriguing involvement of sugar, auxin or abscisic acid (ABA) in events prior to the induction of floral homeotic transcripts. The novel involvement of ABA in the floral transition is further implicated by immunoassay, suggesting an increase in ABA levels in the SAM during this developmental transition. Furthermore, in situ localization, together with in silico data demonstrating a marked enhancement of abiotic stress-related transcripts, such as trehalose metabolism genes in SAMs, points to an overlap of abiotic stress and floral signalling pathways.

SUBMITTER: Wong CE

PROVIDER: S-EPMC2667682 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

Wong Chui E CE Singh Mohan B MB Bhalla Prem L PL

The Plant journal : for cell and molecular biology 20081029 5

The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in the S ...[more]

PMID: 18980639

Similar Datasets

Project description: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.

Project description:BackgroundDespite the importance of the shoot apical meristem (SAM) in plant development and organ formation, our understanding of the molecular mechanisms controlling its function is limited. Genomic tools have the potential to unravel the molecular mysteries of the SAM, and legume systems are increasingly being used in plant-development studies owing to their unique characteristics such as nitrogen fixation, secondary metabolism, and pod development. Garden pea (Pisum sativum) is a well-established classic model species for genetics studies that has been used since the Mendel era. In addition, the availability of a plethora of developmental mutants makes pea an ideal crop legume for genomics studies. This study aims to utilise genomics tools in isolating genes that play potential roles in the regulation of SAM activity.ResultsIn order to identify genes that are differentially expressed in the SAM, we generated 2735 ESTs from three cDNA libraries derived from freshly micro-dissected SAMs from 10-day-old garden peas (Pisum sativum cv Torsdag). Custom-designed oligonucleotide arrays were used to compare the transcriptional profiles of pea SAMs and non-meristematic tissues. A total of 184 and 175 transcripts were significantly up- or down-regulated in the pea SAM, respectively. As expected, close to 61% of the transcripts down-regulated in the SAM were found in the public database, whereas sequences from the same source only comprised 12% of the genes that were expressed at higher levels in the SAM. This highlights the under-representation of transcripts from the meristematic tissues in the current public pea protein database, and demonstrates the utility of our SAM EST collection as an essential genetic resource for revealing further information on the regulation of this developmental process. In addition to unknowns, many of the up-regulated transcripts are known to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation.ConclusionThe presented data provide a picture of the transcriptional profile of the pea SAM, and reveal possible roles of differentially expressed transcripts in meristem function and maintenance.

Project description:Plant growth is the result of cell proliferation in the meristems, which requires a dynamic balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. There is much that remains unknown about this vital developmental process. In this study, we have reported the generation of 2735 ESTs from three cDNA libraries derived from dissected garden pea (Pisum sativum cv Torsdag) shoot apical meristems. Clustering analysis of the resulting sequences gave rise to 1686 non-redundant ESTs. The unique sequences generated together with 500 other pea transcripts randomly selected from the GenBank pea protein database have been utilized to construct a 2K oligonucleotide array. Using this pea array, we have obtained the transcript profiles of pea shoot apical meristems in comparison to non-apical-meristem tissues. A total of 181 or 174 transcripts were identified to be significantly up- or down-regulated in the pea shoot apical meristem, respectively. As expected, close to 61% of the transcripts down-regulated in the shoot apical mersitem are those retrieved from the public database, whereas sequences from the same source only made up 12% of the genes that were expressed at higher levels in SAMs. This revelation highlights the under-representation of transcripts from the meristmatic tissues in the current public protein database. Manual inspection of the list of up-regulated transcripts reveals the presence of sequences predicted to encode products associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and miRNA regulation. Similar genes have been implicated in the regulation of plant stem cell activity. Taken together, our EST collection as well as the microarray data provides useful starting points for more in depth analysis of the meristem function and maintenance. Keywords: shoot apical meristem transcript profiling Total RNA was extracted from dissected SAM (approximately 80 SAMs per extraction) or other plant parts (primary stem, primary roots and mature leaves) using Qiagen RNeasy Mini Kit. Four independent tissue collections and RNA extractions (designated A, B, C and D) were performed for each of the microarray hybridization experiment.The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme (Cochran & Cox, 1992): Sector 1: Cy3-SAM A vs Cy5-NM A Sector 2: Cy5-SAM B vs Cy3-NM B Sector 3: Cy3-SAM C vs Cy5-NM C Sector 4: Cy5-SAM D vs Cy3-NM D

Project description:Knowledge about an organismâs cell and tissue-specific transcriptional repertoire is essential for understanding the gene regulatory circuits that control key developmental events. The shoot apical meristem (SAM) is responsible for development of all the above ground parts of plants. Our understanding of SAM at the molecular level is far from complete. The present work investigates the global gene expression repertoire of SAMs in the garden pea (Pisum sativum). To this end, 10,346 EST sequences representing 7611 unique genes were generated from pea SAM cDNA libraries. These sequences, together with previously reported ESTs, were used to construct a 12K oligonucleotide array used to identify genes exhibiting differential SAM expression, as compared to the axillary meristem, root apical meristem, and non-meristematic tissues. We identified a number of genes that are predominantly expressed in specific cell layers or domains of the SAM, and thus are likely components of the gene networks involved in stem cell maintenance and initiation of lateral organ primordial cells. In situ hybridization confirmed the spatial localisation of some of these key genes within the SAM. Our data also indicate the diversification of some gene expression patterns and functions in legume crop plants. RNA samples were hybridized to two-colour Combimatrix arrays manufactured with a custom library of 11958 probes. The limma software package for R (Smyth, 2005) was used in subsequent statistical analysis of the data generated. On examination of the data during quality control assessment, it became evident that the Cy3 channel showed little dynamic range and background correction and normalisation could not correct for this. Therefore only the Cy5 channel was used in the subsequent analysis. This resulted in somewhat unbalanced sample sizes with six replicates of SAM and one each of RAM, AM and NM. Nevertheless, linear modelling and empirical Bayes moderated t-statistics (Smyth, 2004) used in the statistical analysis allows variance information to be borrowed across both samples and genes, resulting in reliable statistical inference even for the groups with only one sample.

Dataset Information

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

Publications

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets