Identification of QTLs controlling some morphological traits in barley under salinity stress by association mapping

The present study used the association mapping method to identify molecular markers associated with morphological traits using 407 SSR and AFLP markers for 148 barley genotypes. This experiment was carried out as an alpha-lattice design with five incomplete blocks in two replications under normal and salinity stress conditions (EC = 12 ds m-1) at the Agriculture and Natural Resources Research Station, Yazd, Iran. The genetic structure of the population was divided into two subpopulations (K = 2) using the Bayesian method and Structure 2.3.4 software. Association mapping was performed based on a mixed linear model using TASSEL4.3.15 software. Association mapping under normal and salinity stress conditions identified 38 and 43 significant marker-trait associations. Also, several common QTLs for the studied traits were identified. Common markers among traits can be due to pleiotropic effects or linkage between genomic regions involved in these traits. Several QTLs were stable for plant height and flag leaf area in different environmental conditions and can be regarded as stable QTLs. Markers HVM40-144, HVM40-147, HVM40-152, and HVM40-162 for plant height and marker Bmag0606-147 for flag leaf area showed a significant association with these traits in both normal and salinity-stress experiments. So, these QTLs can be suggested as stable gene loci. Identifying major gene loci influencing salinity tolerance in barley can assist in the breeding of salinity tolerance in this crop.