Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. sesquipedalis) under salt stress.

Lei Pan,Jingjie Shao,Tong Gao,Xiaolu Yu,Chen Zeng,Zhichao Liu,Chengzhi Liang,Chanyou Chen,Yu Zheng,Anil Kumar Singh

doi:10.1371/journal.pone.0219799

Abstract

Asparagus bean (Vigna unguiculata ssp. sesquipedalis) is a warm season legume which is widely distributed over subtropical regions and semiarid areas. It is mainly grown as a significant protein source in developing countries. Salinity, as one of the main abiotic stress factors, constrains the normal growth and yield of asparagus bean. This study used two cultivars (a salt-sensitive genotype and a salt-tolerant genotype) under salt stress vs. control to identify salt-stress-induced genes in asparagus bean using RNA sequencing. A total of 692,086,838 high-quality clean reads, assigned to 121,138 unigenes, were obtained from control and salt-treated libraries. Then, 216 root-derived DEGs (differentially expressed genes) and 127 leaf-derived DEGs were identified under salt stress between the two cultivars. Of these DEGs, thirteen were assigned to six transcription factors (TFs), including AP2/EREBP, CCHC(Zn), C2H2, WRKY, WD40-like and LIM. GO analysis indicated four DEGs might take effects on the “oxidation reduction”, “transport” and “signal transduction” process. Moreover, expression of nine randomly-chosen DEGs was verified by quantitative real-time-PCR (qRT-PCR) analysis. Predicted function of the nine tested DEGs was mainly involved in the KEGG pathway of cation transport, response to osmotic stress, and phosphorelay signal transduction system. A salt-stress-related pathway of “SNARE interactions in vesicular transport” was concerned. As byproducts, 15, 321 microsatellite markers were found in all the unigenes, and 17 SNP linked to six salt-stress induced DEGs were revealed. These candidate genes provide novel insights for understanding the salt tolerance mechanism of asparagus bean in the future.

Highlights

Soil salinity is among the leading environmental stresses affecting global agriculture, causing major reductions in crop productivity and quality [1]
Our results indicated that thirteen differentially expressed genes (DEGs) from the 127 leaf-based and 216 rootbased DEGs were assigned to different transcription factors (TFs) families
Four DEGs might be involved in the biological processes of “oxidation reduction”, “transport” and “signal transduction”

Summary

Introduction

Soil salinity is among the leading environmental stresses affecting global agriculture, causing major reductions in crop productivity and quality [1]. This abiotic stressor is a growing problem, affecting approximately 20% of irrigated land and leading to continuing loss of arable areas in the world [2,3]. Salt-tolerant plants uptake and accumulate salt into the cell vacuoles, adjusting the salt concentrations of the cytosol and keeping a high cytosolic K+/Na+ concentration ratio in their cells [6,7,8]. Ion exclusion mechanisms could partly improve plant salt tolerance to relatively low concentrations of NaCl, but would not work at high concentrations of salt [9]

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