Genome-wide analysis of gene expression in soybean shoot apical meristem

Abstract

The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs. The nature of genetic programs and the regulatory networks underlying SAM function in a major legume crop, soybean was investigated here. We used soybean GeneChip (containing 37,744 probe sets) to examine the transcript profiles associated with micro-dissected, actively growing SAMs or growth arrested axillary meristems (AMs) experiencing apical dominance, in comparison to that of non-meristem (NM) tissue. A total of 1,090 and 1,523 transcripts were identified to be significantly up- or down-regulated in the SAM in comparison to the NM. RT-PCR and in situ hybridization analysis were also carried out to verify the experimental approach. The resulting gene expression profiles point to the combinatorial role of diverse regulatory pathways including those associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation in meristem function. In situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene, ANGUSITFOLIA3 that could potentially serve as a novel marker for differentiating cells in the meristem. Computational analysis on the promoter regions of Arabidopsis thaliana orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our data show that plant meristems possess a unique transcriptional profile, with shared "molecular signatures" in apical and axillary meristems providing a rich source of novel target genes for further studies into a fundamental process that impacts plant growth and crop productivity.

RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications

“…To identify PEGs in these meristems (but not specifically in one of them), we grouped similar meristems together and detected 821 genes (20 paralogs). GO annotation indicated that the most enriched categories were associated with flower development and regulation, floral transition from vegetative to reproductive phase, or meristematic phase transition and transcription regulation (Figure  5, in Additional file 2: Tables S23 and S24), which is in good agreement with previous reports in soybean [50,51]. For instance, the PEGs included several homologs of SHORT VEGETATIVE PHASE ( SVP ) that specify the reproductive organ identity and control flowering time in Arabidopsis and rice [52,53] and genes involvement in WUSCHEL ( WUS ) regulatory network essential for SAM maintenance [54].…”

Novel spatial expression of soybean WUSCHEL in the incipient floral primordia

“…The tissue was then dehydrated and embedded in paraplast (Sigma, St Louis, MO, USA) following standard methods. The in situ hybridization was carried out according to modified protocols from Jackson (1991) as described in Haerizadeh et al (2009). Observations and photography were conducted with a microscope BX60 and digital camera DP70 (Olympus, Centre Valley, PA, USA).…”

In VitroPlant Regeneration from Commercial Cultivars of Soybean

“…Recently, there has been a significant effort in understanding the genome of soybean by undertaking large‐scale genome sequencing, microarray, expressed sequence tag sequencing, and transcriptome analyses ([3, 4]; reviewed in Liew et al 2014). In addition, comprehensive studies on synteny, quantitative trait locus (QTL) mapping, and comparative genomics have increased our knowledge on soybean and closely related legumes of economic importance [5–8].…”