Assessment of diversity and validation of microsatellite markesr associated with salinity tolerance in rice (Oryza sativa L.) genotypes

Ten SSR morkers linked to different genes and QTLs responsible for the salinity tolerance in rice, including Saltol QTL which located between zero to 8 CM of the genes, were used to validate their co-segregation with salinity tolerance. Fifty nine diverse rice genotypes including local and improved cultivars mostly from Iran and few exotic rice genotypes were tested during 2009-2011 at Rice Research Institute of Iran, and data were collected on several important traits such as salinity tolerance, seedling height, root dry matter, shoot dry matter and leaf relative water content (RWC). The treatments were: a. control with an electrical conductivity of 0.9 dS.m-1 and b. salinity stress with EC = 12 dS.m-1 for all rice genotypes at seedling stage. Molecular screening for 10 SSR linked marker showed that they amplified 60 alleles among rice genotypes. We identified four SSR markers which significantly co-segregated with at least one trait that was involved in salinity tolerance including; RM315 with seedling height, RM223 with root dry weight and seedling height, RM3627 with root dry weight, seedling height and RWC; and RM8094 with root dry weight and RWC. Molecular data clustering through UPGMA method and Yule coefficient also classified rice genotypes into five major clusters with tolerance to susceptible reactions. As three aforementioned SSR markers; RM315, RM3627 and RM8094 are located on chromosome 1, closely linked to Saltol QTL, and co-segreated with different traits in this experiment, they could be employed to differentiate salinity tolerant rice genotypes in rice breeding programs in Iran.