QTL mapping of genes affecting salt tolerance in rice (Oryza sativa L.) using microsatellite markers

Rice is moderately sensitive to salinity. Salinity affects virtually all aspects of rice growth in varying degree at all stages from germination through maturity. Tolerance to salinity is genetically and physiologically complicated and inherited quantitatively. Application of molecular-marker aided selection technique for improvement of salinity tolerance would accelerate breeding progress by increasing selection efficiency. In order to map the Quantitative Trait Loci (QTLs) for salinity tolerance in rice and determine the contribution of each QTL in phenotypic variation, 63 advanced backcross lines (BC2F5) derived from a cross between IR64 as recurrent parent and Tarom Molaii as donor parent, were used. The phenotypic traits under study included: Sodium(Na) and Potassium(K) concentration in root and shoot, dry and wet weight of root and shoot, Na+:K+ ratio in root and shoot. Polymorphism between the two parents was assesed using 235 SSR markers with uniform coverage on all 12 linkage groups, through which 114 markers showed polymorphism and assigned for genotyping. The map length was 1692.6 cM with an average interval size of 16.3 cM. Transgressive segregation was observed for all traits. We found QTLs with additive effects for K+ in shoot, dry weight of root and shoot, Na+:K+ ratio in root and shoot. At least one QTL was mapped for Na+:K+ ratio in root, on all chromosomes except chromosome 9. All detected QTLs had significant threshold (LOD>4) and also approved by both IM and CIM methods.