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

Background 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. Results Compared 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. Conclusions These 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.