Identification of Candidate Genes that Affect the Contents of 17 Amino Acids in the Rice Grain Using a Genome-Wide Haplotype Association Study

Rice

Research

Zhikang Li¹  Jianlong Xu²  Xiaoqian Wang³  Yunlong Pang³  Jiachuang Fang³  Lihong Xie⁴ 

[1] Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, Guangdong, China;State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 271018, Tai’an, China;State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, National Rice Research Institute, 310006, Hangzhou, China;

关键词: GWAS;    Genome-wide haplotype association study;    Amino acid content;    Candidate genes;   

DOI  :  10.1186/s12284-023-00658-9

 received in 2023-06-24, accepted in 2023-08-27,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe amino acid content (AAC) of the rice grain is one of the most important determinants of nutritional quality in rice. Understanding the genetic basis of grain AAC and mining favorable alleles of target genes for AAC are important for developing new cultivars with improved nutritional quality.ResultsUsing a diverse panel of 164 accessions genotyped by 32 M SNPs derived from 3 K Rice Genome Project, we extracted 1,123,603 high quality SNPs in 44,248 genes and used them to construct haplotypes. We measured the contents of the 17 amino acids that included seven essential amino acids and 10 dispensable amino acids. Through a genome-wide haplotype association study, 261 gene-trait associations containing 174 genes for the 17 components of AAC were detected, and 34 of these genes were associated with at least two components. Furthermore, the associated SNPs in genes were also identified by a traditional genome-wide association study to identify the key natural variations in the specific genes.ConclusionsThe genome-wide haplotype association study allowed us to detected candidate genes directly and to identify key natural genetic variation as well. In the present study, twelve genes have been cloned, and 34 genes were associated with at least two components, suggesting that the genome-wide haplotype association study approach used in the current study is an efficient way to identify candidate genes for target traits. The identified candidate genes, favorable haplotypes, and key natural variations affecting AAC provide valuable resources for further functional characterization and genetic improvement of rice nutritional quality.

【 授权许可】

CC BY   
© Springer Science+Business Media, LLC, part of Springer Nature 2023

【 图 表 】

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