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

Malachy T Campbell,Aaron J Schmitz,Nonoy Bandillo,Aaron J Lorenz,Fouad Razzaq A Al Shiblawi,Qian Du,Sandeep Sharma,Chi Zhang,Kan Liu,Harkamal Walia,Anne-Aliénor Véry

doi:10.1371/journal.pgen.1006823

Abstract

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.

Highlights

Salinity is a widespread limitation for agricultural productivity, especially for irrigated agriculture and coastal lowlands prone to seawater ingress [1,2]
Within the rice diversity panel we observed higher Na+ levels in root tissue in the indica subpopulation compared to japonica 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

Summary

Introduction

Salinity is a widespread limitation for agricultural productivity, especially for irrigated agriculture and coastal lowlands prone to seawater ingress [1,2]. More than 800 million hectares worldwide is affected by salt, which accounts for 6% of the total land area [3]. Besides natural causes such as rising sea levels during the dry and wet cropping seasons, the poor quality of irrigation water and improper drainage, collectively increases soluble salt concentration in the root zone [2,4]. Some rice varieties are most sensitive to salt stress during early tillering and panicle initiation stages of growth [8]. This developmentally-dependent salt-sensitivity, in context of yield reduction, was associated with a significant decrease in tiller number per plant, spikelet number per panicle, fertility, panicle length and primary branches per panicle [7,8,13,14]

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Results

Discussion

Conclusion