Evaluation of haplotype and allelic diversity of SSR markers linked to major effect QTL on chromosome 9 controlling drought tolerance in rice

To study the haplotype and allelic diversity and to identify the informative markers of root characteristics of some rice genotypes under drought stress، 17 microsatellite markers linked to the major QTL located on the rice chromosome 9 controlling root morphologic characteristics under drought stress were used. Based on the genetic data، the studied rice genotypes were assigned into two groups. The genotypes of first group including Bala were more tolerant and the genotypes of other group had lower root characteristics and were more drought sensitive. Results of the molecular analysis showed that RM215 and RM24671 markers at this chromosomal region had the most allelic variation. The association analysis between markers and traits under stress condition were revealed that the SSR markers RM530-A with root thickness (B=0. 431)، RM24627-A with root weight (B=0. 573)، RM24669-C with root number (B=0. 620)، RM6535-C with stem weight (B=-0. 503)، RM684-A with stem length (B=0. 832)، RM160-A with root length (B=0. 373)، RM684-A with genetic code (B=-0. 811) and RM24627-A with biomass (B=1. 073) had the highest standardized regression coefficient and can be used in the breeding programs as informative markers، if the results are confirmed by further experiments. Results of the haplotype analysis divided twenty two genotypes into 16 different haplotypes and the haplotype 8 consisting of Deilamani and IR25571 had the maximum similarity to Bala. It seems that this similar genotypes to Bala be included the QTLs controlling drought tolerance at this genome region. These genotypes can be used for drought tolerance breeding programs after validation of the results in subsequent experiments.