1. Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.)
- Author
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Huainian Liu, Shuangcheng Li, Zhongping Zha, Shiquan Wang, Yuqi Jiang, Xiaoying Ye, Lingxia Wang, Ping Li, Aijun Wang, Yao Liu, Xu Deze, Jun Zhu, Yueyang Liang, Zaijun Zhang, Desuo Yin, Aiping Zheng, Qiming Deng, Ting Zou, Danhua Zhang, Xiaomei Jia, Xinyue Shu, Jianqing Zhu, and Chengzhi Jiao
- Subjects
0106 biological sciences ,Linkage disequilibrium ,Candidate gene ,Population ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Genome-wide association study ,Biology ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,03 medical and health sciences ,Genetics ,Humans ,education ,030304 developmental biology ,Genetic association ,0303 health sciences ,education.field_of_study ,Oryza sativa ,food and beverages ,Oryza ,Plant Breeding ,Phenotype ,Genome, Plant ,010606 plant biology & botany ,Genome-Wide Association Study - Abstract
Rice is one of the most important cereal crops, providing the daily dietary intake for approximately 50% of the global human population. Here, we re-sequenced 259 rice accessions, generating 1371.65 Gb of raw data. Furthermore, we performed genome-wide association studies (GWAS) on 13 agronomic traits using 2.8 million single nucleotide polymorphisms (SNPs) characterized in 259 rice accessions. Phenotypic data and best linear unbiased prediction (BLUP) values of each of the 13 traits over two years of each trait were used for the GWAS. The results showed that 816 SNP signals were significantly associated with the 13 agronomic traits. Then we detected candidate genes related to target traits within 200 kb upstream and downstream of the associated SNP loci, based on linkage disequilibrium (LD) blocks in the whole rice genome. These candidate genes were further identified through haplotype block constructions. This comprehensive study provides a timely and important genomic resource for breeding high yielding rice cultivars.
- Published
- 2020