Salinity is a major factor limiting crop productivity. Rice ( Oryza sativa), a staple crop for the majority of the world, is highly sensitive to salinity stress. To discover novel sources of genetic variation for salt tolerance-related traits in rice, we screened 390 diverse accessions under 14 days of moderate (9 dS·m -1) salinity. In this study, shoot growth responses to moderate levels of salinity were independent of tissue Na + content. A significant difference in root Na + content was observed between the major subpopulations of rice, with indica accessions displaying higher root Na + and japonica accessions exhibiting lower root Na + content. The genetic basis of the observed variation in phenotypes was elucidated through genome-wide association (GWA). The strongest associations were identified for root Na +:K + ratio and root Na + content in a region spanning ~575 Kb on chromosome 4, named Root Na + Content 4 ( RNC4). Two Na + transporters, HKT1;1 and HKT1;4 were identified as candidates for RNC4. Reduced expression of both HKT1;1 and HKT1;4 through RNA interference indicated that HKT1;1 regulates shoot and root Na + content, and is likely the causal gene underlying RNC4. Three non-synonymous mutations within HKT1;1 were present at higher frequency in the indica subpopulation. When expressed in Xenopus oocytes the indica-predominant isoform exhibited higher inward (negative) currents and a less negative voltage threshold of inward rectifying current activation compared to the japonica-predominant isoform. The introduction of a 4.5kb fragment containing the HKT1;1 promoter and CDS from an indica variety into a japonica background, resulted in a phenotype similar to the indica subpopulation, with higher root Na + and Na +:K +. This study provides evidence that HKT1;1 regulates root Na + content, and underlies the divergence in root Na + content between the two major subspecies in rice.
Despite intensive research, few genes have been identified that underlie natural variation for salinity responses in rice. In this study, we used a rice diversity panel for genome wide association mapping to identify HKT1;1 as a factor regulating Na + distribution. Within the rice diversity panel we observed higher Na + levels in root tissue in the indica subpopulation compared to japonica accessions. Three non-synonymous variants were identified within HKT1;1 that were associated with altered Na + accumulation in root tissue, and displayed contrasting frequencies between indica and japonica subspecies. The introduction of HKT1;1 from an indica accession that contained the three non-synonymous variants into a japonica background resulted in a phenotype similar to that exhibited by the indica subpopulation. This work suggests that these allelic variants are likely responsible for the higher root Na + observed in indica accessions. This study has identified a genetic resource for modifying Na + content rice, and provides evidence that HKT1;1 underlies the divergence between indica and japonica subspecies in root Na + content.