Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to SalTol and morpho-physiological characteristics

Knowledge of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. The present study was conducted to evaluate salinity tolerance of Iranian rice varieties. This research was carried out in three separate experiments (control, 6 and 12 dS m−1 NaCl) each based on completely randomized design with 44 rice varieties and three replications. Fourteen days after salt treatments, root and shoot fresh and dry weight, Na+ and K+ concentration, Na+/K+ ratio, root and shoot length, biomass gain, total fresh weight, root/shoot length ratio and shoot/root weight ratio were measured. The varieties were also genotyped for 12 closely linked microsatellite markers to SalTol. Haplotype and association analysis was conducted using these SSR markers for identification of loci related to salt tolerance. The tolerance scores under salinity stress showed that the varieties FL478, Hassani, Gharib, Shahpasand, Nemat, Domzard, Ghasroddashti, Ahlamitarom, Hassansaraee and Binam with more biomass, root and shoot lengths, and low Na+/K+ ratio were tolerant to salinity stress. Association analysis was indicated that there are some informative markers on chromosome 1 in the local and improved Iranian rice varieties genetic background including RM8094, RM1287, AP3206 and RM3412 explaining considerable percentage of the salt tolerance-related traits. These informative markers can be used in future breeding programs such as marker-assisted selection.