Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content

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.
Author summary 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.