title: Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress.
abstract: 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.
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Huizi
authors: H
authors: DuanMu
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Yang
authors: Y
authors: Wang
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Xi
authors: X
authors: Bai
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Shufei
authors: S
authors: Cheng
authors: Department of Biological Sciences, University of Alberta, Edmonton, T6G2E9, Canada.
authors: Michael K
authors: MK
authors: Deyholos
authors: Department of Biological Sciences, University of Alberta, Edmonton, T6G2E9, Canada.
authors: Gane Ka-Shu
authors: GK
authors: Wong
authors: BGI-Shenzen, Shenzhen, 518083, China.
authors: Dan
authors: D
authors: Li
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Dan
authors: D
authors: Zhu
authors: BGI-Shenzen, Shenzhen, 518083, China.
authors: Ran
authors: R
authors: Li
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Yang
authors: Y
authors: Yu
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Lei
authors: L
authors: Cao
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China.
authors: Chao
authors: C
authors: Chen
authors: Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China. ymzhu2001@neau.edu.cn.
authors: Yanming
authors: Y
authors: Zhu
mesh_terms: D000468:Alkalies / Q000633:toxicity*; D018506:Gene Expression Regulation, Plant; D010084:Oxidation-Reduction; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D017693:Sodium Bicarbonate / Q000494:pharmacology; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D000468:Alkalies; D010940:Plant Proteins; D014157:Transcription Factors; D017693:Sodium Bicarbonate
keywords: Alkaline stress; Gene expression profile; RNA sequencing; Stress-responsive genes; Wild soybean