Major rice seedling salinity tolerance QTLs mapped using single nucleotide polymorphism markers (SNPs)
2017
Amas, J.C. | Arceta, M. | Diaz, M.G.Q. | Hernandez, J.E. | Gregorio, G.B.
Salt stress greatly affected rice-growing areas worldwide. The ability of rice to tolerate salt stress at seedling stage is crucial for its early establishment. An F2 population was developed from the cross NSIC RC222 (sensitive) x FL478 (tolerant) to identify putative QTLs associated with salinity tolerance at seedling stage. Results of the phenotypic evaluation indicate shoot Na+ and K+ content, shoot Na-K ratio, root and shoot weight are important parameters in defining levels of salinity tolerance in rice at seedling stage. A genetic map covering 1,359 cm of the rice genome, spaced at an average genetic distance of 10.62 cm was constructed using 128 polymorphic SNP markers. Selective genotyping of extreme phenotypes detected a total of eight major loc (PVE = 15.7-27%). Five of these QTLs were attributed to the tolerant parent, FL478, in which two QTLs were mapped near the known Saltol locus in chromosome 1. The other 6 QTLs in chromosomes 1, 8, 9, 10 and 11 were reported for the first time, suggesting their novelty. Examination of the rice physical map also revealed presence of several genes, typical of salt-stress response within the QTL intervals. The identification of these genomic regions and associated SNP markers can be useful in unraveling mechanisms of salt tolerance in rice and potentially be utilized in breeding.
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