Identification and mapping of quantitative trait loci associated with salinity tolerance in rice [Oryza Sativa] using SSR markers

ABSTRACT

Salinity stress is one of the most widespread soil problems next to drought, in rice growing areas. Reducing Sodium [Na+], while maintaining Potassium [K+] uptake in rice are traits that would aid in salinity tolerance. Therefore, the identification of quantitative trait loci [QTLs] associated with those for Na+ and K+ uptake, will enable breeders to use marker-assisted selection to transfer QTLs into elite lines in rice improvement programs. In view of this, 62 advanced backcross-inbred lines [BILs], at the BC2F5 generation, derived from the cross of Tarome-Molaei [salt tolerant] and Tiqing [Salt sensitive], were used to identify the QTLs involved in salinity stress tolerance, using SSR markers. Advanced backcross inbred lines along with their parents were evaluated for six parameters viz. Sodium [Na+] and Potassium [K+] in roots and shoots and the Na+/K+ ratio, using the modified Yoshida's nutrient solution at an electrical conductivity of 6 and 12 dS/m. A total of 114, out of 235 simple sequence repeats [SSRs] markers that showed polymorphism in the parents, were used to genotype the BILs. A linkage map was constructed with an average interval of 15.3 centiMorgan [cM] between the markers, spanning 1747.3 cM across all 12 rice chromosomes. Using the composite interval mapping [CIM] and a minimum logarithm of the odds [LOD] threshold of 3.0, a total of 14 QTLs were detected as follows; on chromosome 1 [5 QTLs], 3 [1QTL], 4 [3 QTLs], 5 [2 QTLs], 6 [1 QTL], and 8 [2 QTLs] for all six traits except, Sodium [Na+] in the shoot. The phenotypic variation explained by these QTLs ranged from 9 to 30% of the total variation. A QTL [QKr1.2] for K+ content in the root was identified with the highest LOD score [7.8], on chromosome 1. This QTL explicated 30% of the total variation and was identified as a major QTL conferring salt tolerance in rice