Unravelling Morpho‐Physiological Mechanism and Candidate Genes Associated With Salinity Tolerance in Superior Haplotypes of Barley (<i>Hordeum vulgare</i> L.)

ABSTRACT The lack of suitable genetic resources for saline regions and the complexity of the traits involved impede the progress in crop breeding for salt tolerance. The present investigation was carried out using 27 diverse barley genotypes chosen based on the assessment of salt tolerance potential within the barley mini‐core collection at the National Genebank of India. The genotypes were exposed to salinity stress (200 mM NaCl) and were examined for morpho‐agronomic, physiological traits and salt uptake parameters. Exposure to salt stress resulted in a significant decline in all parameters ranging from 5.94% in relative water content to 80.04% in shoot K + /Na + ratio compared to the control in the evaluated accessions. Moreover, the grain yield and its key attribute hundred‐grain weight decreased substantially by 65.35% and 48.62%, respectively, under saline treatment. The majority of the resilient accessions managed to uphold a higher K + /Na + ratio ranging from 0.51 in EC0578359 to 1.19 EC0578251 in contrast to vulnerable germplasm (&lt;0.56) under saline circumstances. The analysis of haplotype variants disclosed allelic diversity linked with two promising candidate genes, HVA1 and HvHKT2 , recognised for conferring salt tolerance. Examination of nucleotide sequences revealed that the HVA1 remained considerably conserved among the evaluated genotypes as the majority of the SNPs (single‐nucleotide polymorphisms) were synonymous. Conversely, for HvHKT2 , a significant level of genetic variation led to the identification of two primary haplotypic clusters—Hap1 associated with sensitivity to salinity and Hap2 linked with tolerant traits. Hap2 predominantly consisted of In/Dels which caused a modification in the overall protein length alongside the phospho‐variant allelic form of the HKT2 gene, further enhancing the biological specificity and functional stress response in a spatiotemporal fashion. These haplotype clusters correlated with favourable traits could be utilised for trait integration into breeding populations, thereby expediting the enhancement of superior salt‐tolerant barley cultivars.