Project description:Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of the saline-alkaline stress transcriptome is most focused on salt (NaCl) stress. Only a little alkaline (NaHCO3) stress transcriptome is limited to one time point after stress. Time-course analysis and comparative investigation on roots in the alkaline stress condition are needed to understand the gene response networks that are subject to alkaline tolerance. We used microarrays to detail the global programme of gene expression underlying NaHCO3 treatment and identified distinct classes of regulated genes during this process. Three week old Glycine soja seedling roots from 3cm root apex were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, roots from three plants originating from the same experiment, condition and cultivar was pooled.

2010-08-14 | E-GEOD-17883 | biostudies-arrayexpress

Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors

Project description:Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO(3) stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO(3) highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (Pâ<â0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response. Young leaves of three-week-old Glycine soja were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, leaves from three plants originating from the same experiment, condition and cultivar was pooled.

2010-10-13 | E-GEOD-20323 | biostudies-arrayexpress

Glycine soja

Project description:Transcriptome Analysis of Wild Soybean (Glycine soja) Infected by Soybean Cyst Nematode

| PRJNA369554 | ENA