Development and validation of candidate gene specific markers for salinity responsiveness in chickpea (Cicer arietinum L.)

Soil salinity is a crucial abiotic stress that significantly reduces the yield and productivity of crops, it reduces chickpea annual yields by 8 to 10% globally. The efficient utilization of marker-aided selection would increase precision and expedite the development of salt-tolerant chickpea varieties. This study intends to identify and analyze microsatellite regions from identified candidate genes related to salinity in chickpeas. A total of 195 putative candidate genes were sort listed, out of which 158 genes contained microsatellite loci with mono- (32%) and di- (32%) nucleotides, followed by tri- (18%), tetra- (11%), penta- (4%) and hexa-nucleotides (3%) motifs for salt tolerance. Gene-based SSR (cg-SSR) primer sets were used to validate the results in a panel of tolerant and sensitive genotypes. The polymorphic cg-SSR loci gave a polymorphic information content (PIC) ranging from 0.21 to 0.37 with an average of 0.34. A neighbor-joining (N-J) tree was created to depict the relationships between genotypes, classifying them into two distinct clusters. The first group was most salt-sensitive, while the second mainly contained salt-tolerant genotypes, which were congruent with the phenotypic data. The analysis of population structure unveiled the presence of two sub-populations. Sub-population 1 consisted of salt-tolerant genotypes, while sub-population 2 comprised salt-sensitive genotypes. The study ultimately revealed that the Cg-SSR markers designed for salinity were effective in deciphering the functional diversity and salinity responses in chickpeas.