QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study

Xiaowu Pan,Xiaoxiang Li,Yonghong Duan,Wenqiang Liu,Yongchao Li,Yaying Yu,Jun Min,Haibo Xiong,Zheng Dong,Sanxiong Liu

doi:10.1038/s41598-020-68742-4

Xiaowu Pan, Xiaoxiang Li + Show 8 more

Open Access

https://doi.org/10.1038/s41598-020-68742-4

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Abstract

Cadmium (Cd) accumulation in rice is a serious threat to food safety and human health. Breeding rice varieties with low Cd accumulation is one of the most effective approaches to reducing health risks from Cd-polluted rice. However, the genetic basis of Cd accumulation in grains, especially in indica rice varieties, has not been fully elucidated. The evaluation of Cd-accumulation capacity was conducted among 338 diverse rice accessions grown in Cd-contaminated soils with different Cd contents. Thirteen rice lines with relatively low Cd accumulation, including six indica rice lines, were identified. Then, 35 QTLs significantly associated with Cd accumulation were identified through sequencing-based SNP discovery and a genome-wide association study (GWAS) in the two experimental years, and only qCd8-1 was detected in both years. Among of them, nine QTLs were co-localized with identified genes or QTLs. A novel QTL, qCd1-3, with the lowest P value was selected for further LD decay analysis and candidate gene prediction. We found differential expression of OsABCB24 between high-Cd-accumulative and low-Cd-accumulative accessions, suggesting it may be a candidate gene for qCd1-3 associated with low Cd accumulation. These results may be helpful for further exploiting novel functional genes related to Cd accumulation and developing rice variety with low Cd accumulation through marker-assisted breeding.

Highlights

Cadmium (Cd) accumulation in rice is a serious threat to food safety and human health
In order to accurately evaluate the Cdaccumulation capacity among different genetic rice lines, we cultivated 338 rice lines in paddy fields that naturally contained different concentrations of cadmium, and the experiment was conducted in two consecutive years
Because pH is probably the most important influencing factor of Cd uptake in rice p lants[34], it is reasonable to ascribe this difference in grain Cd content to the difference in pH

Summary

Introduction

Cadmium (Cd) accumulation in rice is a serious threat to food safety and human health. We found differential expression of OsABCB24 between high-Cd-accumulative and low-Cd-accumulative accessions, suggesting it may be a candidate gene for qCd1-3 associated with low Cd accumulation These results may be helpful for further exploiting novel functional genes related to Cd accumulation and developing rice variety with low Cd accumulation through marker-assisted breeding. Using a composite method combining GWAS and other analyses, Yan et al.[10] found that a missense mutation in OsCd1 resulted in the indica-japonica differentiations of Cd accumulation in rice grain These reports clearly demonstrate that GWAS is an effective approach to elucidate the genetic mechanism underlying Cd accumulation. For HMA3 and most of these Cd-related QTLs, the favorable alleles for reducing Cd accumulation were basically derived from japonica rice varieties and limited their breeding application in indica rice

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