Journal of Crop Breeding

In order to investigate of genetic diversity and association analysis SSR markers and related traits to cold tolerance in rice, 22 rice genotypes including 10 landrace and improved and 12 foreign genotypes and 21 SSR markers were used. In total, 89 alleles were found. The number of alleles at each locus ranged from 2 to 7. The highest number of alleles was observed in primer RM8231 and minimum number of alleles in primer RM119. The maximum of polymorphic information content (0.7486) was related to RM8231 and the lowest (0.2573) was related to RM7424. The gene diversity rate varied between the lowest value is 0.2777 (RM7424) to the maximum value 0.78 to (RM8231). The used microsatellites revealed relatively high polymorphism and suggest theses loci have high potential in distinction of genotypes. The association analysis based on stepwise regression of SSR data and phenotypic data identified totally 14 positive and informative alleles for length and weight of root and stem under normal and stress condition. The highest coefficient and determination under stress was found for root length with two alleles of RM1337-A and RM5774-C. Also no alleles were detected associated with root weight under stress. The identified informative markers in the present study can be used for breeding projects if confirmed in subsequent experiments.