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. 2023 Sep 15;16(1):40.
doi: 10.1186/s12284-023-00658-9.

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

Xiaoqian Wang  1 , Lihong Xie  2 , Jiachuang Fang  1 , Yunlong Pang  3 , Jianlong Xu  4   5 , Zhikang Li  6
Affiliations

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

Xiaoqian Wang et al. Rice (N Y). .

Abstract

Background: The 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.

Results: Using 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.

Conclusions: The 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.

Keywords: Amino acid content; Candidate genes; GWAS; Genome-wide haplotype association study.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The amino acid contents (A) and correlations (B) among the 17 amino acids studied in the association panel
Fig. 2
Fig. 2
Genotype distribution and the population structure of the accessions in the rice association panel. (A) The distribution of SNPs with minor allele frequency > 0.05 and missing data rate ≤ 20% on the 12 rice chromosomes. (B) The number of haplotypes for the 44,248 genes covered by the SNPs. (C) Screen plot from the STRUCTURE analysis showing the selection of Q for the association study. (D) Bayesian clustering of the 164 accessions performed using STRUCTURE. (E) Population structure revealed by 3D principal component analysis. (F) Population structure revealed by kinship analyses
Fig. 3
Fig. 3
The Manhattan and QQ plots from the genome-wide haplotype association study for the 17 components of amino acid contents in rice
Fig. 4
Fig. 4
The gene-trait associations detected by the genome-wide haplotype association study and the key natural sequence variants in two candidate genes on chromosomes 3 and 9 of rice. (A) The local Manhattan plot on chromosome 3 of genome-wide haplotype association study for Cys. (B) The haplotype test of LOC_Os03g25350 associated with Cys. (C) The natural variation of LOC_Os03g25350 and its association with Cys. (D) The local Manhattan plot on chromosome 9 of genome-wide haplotype association study for the seven amino acids. (E) The haplotype test of LOC_Os09g23380 associated with the seven amino acids. (F) The natural variation of LOC_Os09g23380 and its associations with the seven amino acids
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