QTL mapping and candidate gene analysis of cadmium accumulation in polished rice by genome-wide association study
Open Access
- 16 July 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Scientific Reports
- Vol. 10 (1), 1-11
- https://doi.org/10.1038/s41598-020-68742-4
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.This publication has 61 references indexed in Scilit:
- Genome-wide efficient mixed-model analysis for association studiesNature Genetics, 2012
- Low-affinity cation transporter ( OsLCT1 ) regulates cadmium transport into rice grainsProceedings of the National Academy of Sciences of the United States of America, 2011
- Tonoplast-localized Abc2 Transporter Mediates Phytochelatin Accumulation in Vacuoles and Confers Cadmium ToleranceOnline Journal of Public Health Informatics, 2010
- Genome-wide association studies of 14 agronomic traits in rice landracesNature Genetics, 2010
- Gene limiting cadmium accumulation in riceProceedings of the National Academy of Sciences of the United States of America, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Principal components analysis corrects for stratification in genome-wide association studiesNature Genetics, 2006
- A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics, 2005
- Haploview: analysis and visualization of LD and haplotype mapsBioinformatics, 2004