Identification of QTLs for Seedling Salinity Tolerance in Rice (Oryza sativa) Using Ultra-High Density SNP Markers.

Rice is one of the most important cereals that feed more than half of the world’s population. However, production of rice is faced with many challenges like the problem on salinity. Many studies in the past have been conducted to identify quantitative trait loci (QTLs) linked to salinity tolerance. However, due to limited number of polymorphic markers, most of the reported QTLs are still covering huge chromosomal intervals. Hence, the use of those QTLs for breeding purposes is still limited or not being adopted at all.  In this study, the main objective is to construct a high-density rice genetic map for identification of QTLs and candidate genes for salinity tolerance. We characterized a population of 230 recombinant inbred lines developed from Bengal and Pokkali cross for traits related to salinity tolerance. The population and the parents were also genotyped by genotyping-by-sequencing (GBS).   After implementing a filtering method, a total of 9,303 SNP markers were used to construct a linkage map. For the nine traits we investigated under salt stress, thirty-six QTLs were detected, of which, eight were large-effect QTLs and the rest were small effect QTLs. On the average, the interval size of the QTL is about 132 kilo base pairs. Interestingly, genes located within the QTLs indicated the importance of transporters, osmotic regulators, transcription factors, and protein kinases in the fitness of rice under salt stress. Overall, the saturation of SNP markers in our linkage map increased the resolution of QTL mapping similar to fine mapping. Our study offers new insights on salinity tolerance and presents useful candidate genes that will help in gene pyramiding and marker-assisted breeding for development of salt tolerant rice varieties.