Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)

Hongmei Zhang,Xiaoqing Liu,Jingbin Chen,Xin Chen,Huatao Chen,Wenjing Xu,Shouping Yang

doi:10.1186/s12863-021-00989-w

Hongmei Zhang, Xiaoqing Liu + Show 5 more

Open Access

https://doi.org/10.1186/s12863-021-00989-w

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Abstract

BackgroundHigh salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions.ResultsCompared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in “Glycolysis/Gluconeogenesis” (ko00010), “Cutin, suberine and wax biosynthesis” (ko00073), and “phenylpropanoid biosynthesis” (ko00940) in Sujiang 1419, although “cysteine/methionine metabolism” (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties.ConclusionsThese findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis.

Highlights

High salinity is a devastating abiotic stresses for crops
These findings show a limited set of differentially expressed genes (DEGs), primarily transcription factors (TFs), respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis
Transcriptome sequencing and discovery of novel transcripts The Illumina HiSeqTM 2000 platform was used to sequence Suzi 41 and Sujiang 1419 transcriptomes in yardlong bean that were treated under high salt stress conditions (41S and Sujiang 1419 salt-stressed (1419S)) to compare with those of unstressed plants (41C and Sujiang 1419 control (1419C)) in order to identify differences in their transcriptional responses to high salinity by these two phenotypically different varieties

Summary

Introduction

High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. Salt-tolerant plants characteristically exhibit adaptive maintenance of intracellular ion homeostasis, and in particular, the salt overly sensitive (SOS) pathway has been implicated in maintaining a K+/ Na+ ratio essential for growth under high salinity conditions. The SOS pathway involves regulation of ion transport by the SOS1 Na+/H+ plasma membrane antiporter, which is activated via the SOS3 calcium sensor and SOS2 Ser/Thr protein kinase [5, 6]. Transcription factors from several families participate in ion homeostasis and salt tolerance through regulation of signal transduction pathways and downstream transporters, such as apetala2/ethylene responsive factor (AP2/ERF), dehydration responsive element binding protein (DREB), basic leucine zipper domain (bZIP), WRKY, and MYB, among others [8,9,10,11,12]

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