Gene expression and genome-wide association analyses identify suitable targets for salinity tolerance in chickpea

Abstract

Chickpea is an important source of protein for developing countries, but it is highly susceptible to salt stress, which significantly affects its growth and yield. This study investigates the genetic and molecular mechanisms of salt tolerance in chickpea by integrating genome-wide association studies (GWAS) and gene expression analyses. Gene expression data were analyzed from three chickpea datasets to identify genes associated with salt stress. A total of 97 differentially expressed genes (DEGs) were identified (FDR < 0.05), including key genes involved in abscisic acid signaling, the dehydration response and cell wall modification, such as TPS2, NCED1, CDF1, DHN3 and NAC7. A GWAS analysis utilizing SNP genotyping data from 679 chickpea accessions and 11 agronomic traits revealed significant associations (p < 0.001) between SNPs within the DEGs identified in the previous analysis and key agronomic traits, including days to maturity, plant height, and seed weight. Among them, 13 DEGs were specifically associated with traits such as yield and flowering time. Finally, qPCR analysis confirmed the differential expression of eight genes in root tissues under different salinity conditions. Patatin-1-Kuras 2-like had the highest expression levels, with a 20–24-fold increase in response to salinity. Other genes such as NCED1 and CDF1 were upregulated at lower salt concentrations (50 mM NaCl), while TPS3 and drKD showed reduced expression at higher concentrations (150 mM NaCl). In conclusion, this study provides a comprehensive understanding of the genetic and molecular basis of salt tolerance in chickpea and highlights key genes and pathways that may serve as valuable targets for the development of salt-resistant cultivars and ultimately contribute to improved crop productivity and food security in salt-stressed regions.