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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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12863-021-00989-w.

bmc genomic data

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