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

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PLoS genetics, ISSN: 1553-7404, Vol: 13, Issue: 6, Page: e1006823

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10.1371/journal.pgen.1006823; 10.1371/journal.pgen.1006823.g002; 10.1371/journal.pgen.1006823.t002; 10.1371/journal.pgen.1006823.g005; 10.1371/journal.pgen.1006823.g001; 10.1371/journal.pgen.1006823.g004; 10.1371/journal.pgen.1006823.t001; 10.1371/journal.pgen.1006823.g007; 10.1371/journal.pgen.1006823.g003; 10.1371/journal.pgen.1006823.g008; 10.1371/journal.pgen.1006823.g006
Malachy T. Campbell; Nonoy Bandillo; Fouad Razzaq A. Al Shiblawi; Sandeep Sharma; Kan Liu; Qian Du; Aaron J. Schmitz; Chi Zhang; Anne-Aliénor Véry; Aaron J. Lorenz; Harkamal Walia; Julian I. Schroeder Show More Hide
Public Library of Science (PLoS); Figshare
Agricultural and Biological Sciences; Biochemistry, Genetics and Molecular Biology; Medicine; Genetics; Ecology; Sociology; Developmental Biology; 110309 Infectious Diseases; Plant Biology; 59999 Environmental Sciences not elsewhere classified; 69999 Biological Sciences not elsewhere classified; HKT; indica subpopulation; 4.5 kb fragment; root sodium content Salinity; GWA; RNC 4; root Na; RNA; CDS; salt tolerance-related traits
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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.