Utilization of SNP-based Highly Saturated Molecular Map of a RIL Population for the Detection of QTLs and Mining of Candidate Genes for Salinity Tolerance in Rice

Abstract

Purpose : Previously, QTL hotspots were identified for salt tolerance from a RIL population of At354 x Bg352, under a temperature-controlled environment at the International Rice Research Institute, Philippine. However, as the rice-growing environment in Sri Lanka experiences salinity stress exaggerated with high temperature, the importance of revealing QTLs under such environment of a tropical region was realized. Therefore, the present study was focused to examine QTLs under such environment, deploying SNP-based molecular map, and retrieving potential candidate genes underlying the QTLs. Research Method : RIL population was assessed at 12 dSm-1 electrical conductivity coupled with average temperature ranged from 38 to 32 °C, day and night, respectively. QTLs were mapped using SNP markers. Potential candidate genes were identified using NGS-based high-throughput QTL-seq strategy employing whole-genome re-sequencing data of At354 and Bg352 and Gene Ontology approach. Findings : The results revealed a broad spectrum of phenotypic variation and a significant coefficient of correlation among the morpho-physiological traits in the RIL population. Four QTLs were revealed on chromosome 7, 9, and 11 for shoot Na+ concentration (qSNC7), shoot K+ concentration (qSKC9), shoot Na+/ K+ ratio (qSNK9) and root length (qRL11). Five genes, Os07g0635900, Os07g0637300, Os09g0330000, Os11g0514500, and Os11g0523800 within novel QTLs with polymorphic variants between At354 and Bg352, were recognized as potential candidate genes regulating salinity stress. Originality / Value : The putative candidate genes have been reported to be involved in cellular transmembrane and growth modulating functions under stress, indicating their usefulness to be further researched.