Genetic dissection of epistatic and QTL by environment interaction effects in three bread wheat genetic backgrounds for yield-related traits under saline conditions

Salt stress represents a major impediment to global wheat production. Development of wheat varieties that offer tolerance to salt stress would increase productivity. Here we report on the results of a genetic study of salt tolerance in bread wheat across multiple genetic backgrounds and environments, with the goal of identifying quantitative trait loci (QTLs) for 9 yield-related traits that are both genetic background independent and environmentally stable. Three RIL populations derived from crosses between a super salt tolerant landrace (Roshan) and 3 bread-wheat cultivars (Falat, Sabalan, Superhead#2) that vary in salt tolerance were phenotyped in three environments. Genetic maps were constructed for each RIL population and independent analyses of each population/environment combination revealed significant associations of 92 genomic regions with the traits evaluated. Joint analyses of yield-related traits across all populations revealed a strong genetic background effect, with no QTLs shared across all genetic backgrounds. Fifty-seven QTLs identified in the independent analysis co-localized with those in the joint analysis. Overall, only 3 QTLs displayed significant epistatic interactions. Additionally, a total of 67 QTLs were identified in QTL analysis across environments, two of these (QSPL.3A, QBYI.7B-1) were both stable and not reported previously. Such novel and stable QTLs may accelerate marker-assisted breeding of new highly productive and salt tolerant bread-wheat varieties.