The isolation and identification of some rice (Oryza sativa L.) lines and hybrids using molecular markers associated with cold tolerance

In this study, 24 SSR markers associated with QTL controlling cold tolerance and four markers associated with cold genes were used to determine the genetic affinity of nine parental lines (including four Iranian susceptible lines and five tolerant IRRI lines) and their 20 hybrid combinations to cold stress. The Evaluation of relationship between SSR markers associated with QTLs controlling cold tolerance with susceptible and tolerant genotypes indicated that RM292, RM261, RM270, RM263, RM283, RM7200, RM7003, RM239 RM6770, RM101 and RM335 were able to separate four Iranian susceptible genotypes from five IRRI tolerant genotypes. Hassani and Binam genotypes had the most and the least similarity with IRRI genotypes, respectively. Markers associated with cold genes didn’t show any polymorphism between parents. Among the 24 used SSR markers, 18 markers were polymorph that amplified 51 polymorphic bands. The maximum band number (six and five) was produced by RM84 and RM202, respectively. The minimum band number (two) was produced by RM335, RM292, RM420, RM341, RM261, RM270 and RM283. PIC value for SSR primers varied from 0.25 to 0.40. Cluster analysis using UPGMA based on SSR markers and simple matching coefficient separated 9 parental lines and their 20 hybrid combinations into four groups, including 6, 5, 15 and 3 genotypes, respectively. Totally, hybrids were more similar to the IRRI genotypes. Results of canonical discriminant function Analysis using the Fisher’s linear method showed that the UPGMA method separated the genotypes with the 93.1  accuracy.