DOI:
10.1371/journal.pgen.1006823
Author(s):
Malachy T. Campbell; Nonoy Bandillo; Sandeep Sharma; Aaron J. Schmitz; Aaron J. Lorenz; Harkamal Walia; Fouad Razzaq A. Al Shiblawi; Anne Aliénor Véry; Kan Liu; Qian Du; Chi Zhang Show More Hide
Tags:
Agricultural and Biological Sciences; Biochemistry, Genetics and Molecular Biology; Medicine
article description
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) salinity. In this study, shoot growth responses to moderate levels of salinity were independent of tissue Nacontent. A significant difference in root Nacontent was observed between the major subpopulations of rice, with indica accessions displaying higher root Naand japonica accessions exhibiting lower root Nacontent. The genetic basis of the observed variation in phenotypes was elucidated through genome-wide association (GWA). The strongest associations were identified for root Na:Kratio and root Nacontent in a region spanning ~575 Kb on chromosome 4, named Root NaContent 4 (RNC4). Two Natransporters, 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 Nacontent, 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 Naand Na:K. This study provides evidence that HKT1;1 regulates root Nacontent, and underlies the divergence in root Nacontent between the two major subspecies in rice.