期刊
SCIENCE CHINA-LIFE SCIENCES
卷 65, 期 4, 页码 781-794出版社
SCIENCE PRESS
DOI: 10.1007/s11427-020-1960-9
关键词
genotype imputation; GWAS; Fine mapping; causal mutation; pig
类别
资金
- National Natural Science Foundation of China [31640046, 31760656]
- National Key Research and Development Program of China [2020YFA0509500]
Sequencing-based GWAS have proven useful in identifying causal associations between genetic variants and traits. In this study, genotype imputation was used to increase SNP density in a large-scale swine F-2 population, revealing key nucleotides influencing traits and proposing two candidate genes related to meat traits. The study also illustrated various scenarios researchers may encounter in imputation-based GWAS.
Sequencing-based genome-wide association studies (GWAS) have facilitated the identification of causal associations between genetic variants and traits in diverse species. However, it is cost-prohibitive for the majority of research groups to sequence a large number of samples. Here, we carried out genotype imputation to increase the density of single nucleotide polymorphisms in a large-scale Swine F-2 population using a reference panel including 117 individuals, followed by a series of GWAS analyses. The imputation accuracies reached 0.89 and 0.86 for allelic concordance and correlation, respectively. A quantitative trait nucleotide (QTN) affecting the chest vertebrate was detected directly, while the investigation of another QTN affecting the residual glucose failed due to the presence of similar haplotypes carrying wild-type and mutant allelesin the reference panel used in this study. A high imputation accuracy was confirmed by Sanger sequencing technology for the most significant loci. Two candidate genes, CPNE5 and MYH3, affecting meat-related traits were proposed. Collectively, we illustrated four scenarios in imputation-based GWAS that may be encountered by researchers, and our results will provide an extensive reference for future genotype imputation-based GWAS analyses in the future.
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