Genome wide association study and haplotype analysis reveals the role of HvHKT1;5 in potassium retention but not Na+ exclusion in barley (Hordeum vulgare L.)

Salinity stress is one of the major abiotic stresses which affect grain yield and quality in crops. Identifying and exploring the QTL/genes and elite alleles that control salt tolerance is crucial for breeding salt-tolerant crop varieties. In this study, a diverse panel of 214 barley (Hordeum vulgare L.) accessions were used to identify quantitative trait loci (QTL) for salt tolerance and Na+ and K+ content in leaves under salt stress by MLM model and MapQTL6.0 software. Significant correlations between leaf ion content and salt tolerance were observed. One major QTL, Q.SL.2H, was identified on chromosome 2H and was responsible for the overall salinity tolerance through regulating Na+ exclusion under salt stress. The other major QTL was detected on chromosome 4H that overlapped with HvHKT1;5 gene and was responsible for K+ retention in leaves. Several other minor QTL were detected by MapQTL that could help in selecting salt-tolerant varieties. The haplotype analysis showed that amino acid substitutions of HvHKT1;5 in exon2 at 416 and 438 may have contributed to K+ retention under salinity stress. These findings indicate the existence of two major mechanisms for salinity tolerance determined by two major QTL and challenge the accepted views on the role of HvHKT1;5 transporters in Na+ exclusion in barley adaptive response to salinity stress.