Mapping salinity tolerance genes in rice (Oryza sativa L.) at reproduction stage

Microsatellite or simple sequence repeats (SSR) was the marker-aided selection (MAS) technique utilized to determine salinity tolerance in rice. It accelerates the rice breding 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 F8 recombinant inbred lines (RILs) of IR29. Phenotying 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 atthe IRRI [International Rice Research Inst., Los Baños, Laguna, Philippines] 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 markers 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 biomass weight (RBWT), three 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, 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, 17.62-24.7 4% for RTBWT, and 16.24-28.6% for seedling tolerance with higher logarithm of odds (LOD) while less 3.0. The QTLs detected among the traits (RFGWT, RBWT and RTWT) 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.