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

Scientific Reports
Xiaowu PanXiaoxiang Li

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 b...Continue Reading

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Citations

Oct 7, 2021·The New Phytologist·Joanna Banasiak, Michał Jasiński

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Methods Mentioned

BETA
transgenic
atomic-absorption spectrometry
atomic absorption spectrometry
PCA
PCR

Software Mentioned

GEMMA
Burrows Aligner ( BWA )
ADMIXTURE
GATK
HaploView
STRUCTURE
R package qqman
Pophelper
EIGENSOFT
Plink

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