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Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans

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. In this study, we addressed the nature of SAM gene networks involved in the early floral initiation process in the crop legume soybean. Unique aspects (such as pod development and nitrogen fixation) of legume development make them appealing for plant development studies. Soybean, a major oilseed crop, possesses varied maturity groups; hence, understanding and unravelling initial transition control has implications in manipulating crop yield. To this end, we performed global gene expression analysis using Affymetrix® soybean GeneChip® with RNA isolated from micro-dissected soybean SAMs at various time points after plants were shifted from long-day to short-day growth conditions. Analysis of the resulting microarray data revealed a total of 331 transcripts that have differential expression profiles. Intriguingly, about 20% of the transcripts affected by the switch in the development program have orthologs reported to be responsive to abscisic acid (ABA), suggesting an increase in ABA levels in the SAM during this developmental change. A subsequent immunoassay verified this, thereby implicating its possible function as an endogenous signal during the floral evocation process. The striking occurrence of abiotic stress-related transcripts, including trehalose metabolism genes, in SAMs during the early transition to floral meristems points to an overlap of abiotic stress and floral signalling pathways in soybean. In addition, other hormones - auxin, jasmonic acid and brassinosteroids - and a number of candidate protein kinases may also act in the signalling process prior to or concurrently with the induction of the putative floral homeiotic transcripts. This indicates that molecular events mediated by multiple hormonal pathways are part of the mechanism employed by soybean to regulate the floral transition process. Keywords: transcript profiling floral transition soybean shoot apical meristem

ORGANISM(S): Glycine max

PROVIDER: GSE10251 | GEO | 2009/01/17

SECONDARY ACCESSION(S): PRJNA108439

REPOSITORIES: GEO

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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.

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:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Experiment Overall Design: Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.

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Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans

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