Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress

Funct Integr Genomics. 2015 Nov;15(6):651-60. doi: 10.1007/s10142-015-0439-y. Epub 2015 Apr 15.


Soil alkalinity is an important environmental problem limiting agricultural productivity. Wild soybean (Glycine soja) shows strong alkaline stress tolerance, so it is an ideal plant candidate for studying the molecular mechanisms of alkaline tolerance and identifying alkaline stress-responsive genes. However, limited information is available about G. soja responses to alkaline stress on a genomic scale. Therefore, in the present study, we used RNA sequencing to compare transcript profiles of G. soja root responses to sodium bicarbonate (NaHCO3) at six time points, and a total of 68,138,478 pairs of clean reads were obtained using the Illumina GAIIX. Expression patterns of 46,404 G. soja genes were profiled in all six samples based on RNA-seq data using Cufflinks software. Then, t12 transcription factors from MYB, WRKY, NAC, bZIP, C2H2, HB, and TIFY families and 12 oxidation reduction related genes were chosen and verified to be induced in response to alkaline stress by using quantitative real-time polymerase chain reaction (qRT-PCR). The GO functional annotation analysis showed that besides "transcriptional regulation" and "oxidation reduction," these genes were involved in a variety of processes, such as "binding" and "response to stress." This is the first comprehensive transcriptome profiling analysis of wild soybean root under alkaline stress by RNA sequencing. Our results highlight changes in the gene expression patterns and identify a set of genes induced by NaHCO3 stress. These findings provide a base for the global analyses of G. soja alkaline stress tolerance mechanisms.

Keywords: Alkaline stress; Gene expression profile; RNA sequencing; Stress-responsive genes; Wild soybean.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkalies / toxicity*
  • Gene Expression Regulation, Plant*
  • Oxidation-Reduction
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Plant Roots / drug effects
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • Sodium Bicarbonate / pharmacology
  • Soybeans / genetics*
  • Soybeans / metabolism
  • Stress, Physiological / genetics*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • Alkalies
  • Plant Proteins
  • Transcription Factors
  • Sodium Bicarbonate