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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.

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