Abstract
Microsatellite or simple sequence repeats (SSR) was the marker-aided selection (MAS) technique utilized to determine salinity tolerance in rice. It accelerates the rice breeding process by significantly improving selection efficiency. Tagging genes for salinity tolerance in rice is an important step in identifying candidate markers flanking the genes. The genes for salinity tolerance in Pokkali were mapped utilizing the F, recombinant inbred lines (RILS) of IR29. Phenotyping of 80 RILS and their parents (IR29/Pokkali) at the seedling stage was done using salinized (EC = 12 dS/m) culture solution under controlled conditions at the IRRI Phytotron and at the reproductive stage using salinized (EC = 5 dS/m) water at the IRRI greenhouse. The 12-linkage group map, which was constructed using 93 microsatellite markers, collectively covered 2433.3 CM at an average interval between markers of 25.39 CM. Quantitative trait loci (QTL) mapping determined the positions and effects of QTL for yield components and traits associated with salt tolerance in rice. Single marker analysis and interval mapping were combined in the QTL analysis procedures and all approaches showed similar QTL detection results. QTLs associated with salinity tolerance at the reproductive and seedling stages were tagged on chromosomes 1, 3, 4, 7 and 9. Two QTLs were identified for percent reduction of filled grain weight (RFGWT), four QTLs for percent reduction of biomass weight (RBWT), three QTLs for percent reduction of total biomass weight (RTBWT), and three QTLs for seedling stage tolerance. Common QTLs for the three quantitative traits (RFGWT, RBWT, and RTBWT) for salinity tolerance were observed in chromosomes 7 and 9 at the reproductive stage. Common QTLs for RBWT and RTBWT were also detected in chromosomes 4, 7, and 9. The proportions of phenotypic variations explained by each QTL ranged from 17.23 to 21.25% for RFGWT, 16.53-39.07% for RBWT, 17.62-24.74% for RTBWT, and 16.24-28.6% for seedling tolerance with higher logarithm of odds (LOD) value of >3.0. The QTLs detected among the traits (RFGWT, RBWT and RTBWT) at the reproductive stage and the salt stress rating at seedling stage did not share the same map locations, suggesting that the genes controlling salinity tolerance at the seedling and reproductive stages of rice are different.