Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies

Han Yan ,Jinjie Li,Xueqiang Wang,Hongliang Zhang,Zhendong Tian ,Fengmei Li,Xiuni Lin,Liang Sun,Changhua Dai,Lu Feng,Jianyin Xie,Xiaoyang Zhu,Caiyan Chen,Chuang Xu ,Zhanying Zhang,Wenxiu Xu,Ming Ma ,Yongfei Gao ,Ting Li,Liang Wu ,Zhenyan He

doi:10.1038/s41467-019-10544-y

Abstract

Cadmium (Cd) accumulation in rice grain poses a serious threat to human health. While several transport systems have been reported, the complexity of rice Cd transport and accumulation indicates the necessity of identifying additional genes, especially those that are responsible for Cd accumulation divergence between indica and japonica rice subspecies. Here, we show that a gene, OsCd1, belonging to the major facilitator superfamily is involved in root Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain Cd accumulation between indica and japonica. Near-isogenic line tests confirm that the indica variety carrying the japonica allele OsCd1V449 can reduce the grain Cd accumulation. Thus, the japonica allele OsCd1V449 may be useful for reducing grain Cd accumulation of indica rice cultivars through breeding.

Highlights

By over-expression of the functional OsHMA3 or the disruption of OsLCT1 and OsHMA2, the grain Cd content can be reduced to some extent, which gives a clue that rice grain Cd contents can be reduced through regulating transporters expression
We combined data from genome-wide association studies (GWAS), gene annotation in gene ontology (GO) Slim database and the yeast assay to look for genes associated with rice grain Cd accumulation
Using 3,291,150 single-nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) > 0.05 covering the whole rice genome, we performed GWAS to identify the genetic loci associating with grain Cd accumulation

Summary

Introduction

By over-expression of the functional OsHMA3 or the disruption of OsLCT1 and OsHMA2, the grain Cd content can be reduced to some extent, which gives a clue that rice grain Cd contents can be reduced through regulating transporters expression. The rice Cd transport mechanism is complex and grain Cd accumulation is a result of cooperative interactions among multiple cells and issues. It is, worthwhile to explore more genetic loci involving in Cd accumulation of rice grain. The natural allelic variations responsible for rice varietal differences have not been fully explored and the genetic basis of grain Cd accumulation differences remains unknown. The natural variation OsCd1V449 in japonica, which is associated with a reduced Cd transport ability and decreased grain Cd accumulation, shows a potential value in low-Cd rice selection

Methods

Results

Conclusion