Dissecting the Genetic Basis of Salt Tolerance in Rice (Oryza sativa)

Excessive salt is a major factor limiting crop productivity. Rice is an important food crop worldwide, and provides a major source of calories for billions of people in tropical and subtropical developing countries. In many regions throughout Southeast Asia, rice is grown in low-lying coastal regions, which are prone to ingress by seawater. Rice is highly sensitive to salt stress, with mild salinity resulting in large reductions in yield. Improving salt tolerance in rice is essential for ensuring food security for many individuals throughput the developing world. In this work, the overall goals were to characterize a diverse collection of cultivated rice for salt tolerance, and elucidate the genetic basis of salt tolerance-related traits. To this end, a multidisciplinary approach that combined aspects of classical plant physiology, molecular biology, computational biology, and quantitative genetics was employed. Considerable natural variation was observed for salt-tolerance related traits. Moreover, the five subpopulations of rice (indica, temperate japonica, tropical japonica, aromatic, and aus) exhibited contrasting phenotypes, suggesting that there may be inherent differences between the subpopulations of cultivated rice for salt tolerance. Phenotypes derived from classical end-point phenotyping, and temporal non-destructive imaging, were used for genome-wide association mapping. For the majority of the traits analyzed, numerous loci were identified that accounted for only a small portion of the phenotypic variation. These results indicate that many genes collectively contribute to salt-tolerance in rice. However, a single gene, HKT1;1, was identified and was shown to regulate root sodium content. Moreover, variants of HKT1;1 were shown to underlie the divergence of Indica and Japonica subspecies of rice for root Na+ content. Transcriptome data from 91 diverse accessions of the rice diversity panel were leveraged to elucidate the genetic mechanisms underlying the complex salt tolerance-related traits. Together, this work provides a comprehensive phenotypic and genetic analysis of the responses to moderate salinity