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Wei C, Chang C, Zhang W, Ren D, Cai X, Zhou T, Shi S, Wu X, Si J, Yuan X, Li J, Zhang Z. Preselecting Variants from Large-Scale Genome-Wide Association Study Meta-Analyses Increases the Genomic Prediction Accuracy of Growth and Carcass Traits in Large White Pigs. Animals (Basel) 2023; 13:3746. [PMID: 38136785 PMCID: PMC10740834 DOI: 10.3390/ani13243746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Preselected variants associated with the trait of interest from genome-wide association studies (GWASs) are available to improve genomic prediction in pigs. The objectives of this study were to use preselected variants from a large GWAS meta-analysis to assess the impact of single-nucleotide polymorphism (SNP) preselection strategies on genome prediction of growth and carcass traits in pigs. We genotyped 1018 Large White pigs using medium (50k) SNP arrays and then imputed SNPs to sequence level by utilizing a reference panel of 1602 whole-genome sequencing samples. We tested the effects of different proportions of selected top SNPs across different SNP preselection strategies on genomic prediction. Finally, we compared the prediction accuracies by employing genomic best linear unbiased prediction (GBLUP), genomic feature BLUP and three weighted GBLUP models. SNP preselection strategies showed an average improvement in accuracy ranging from 0.3 to 2% in comparison to the SNP chip data. The accuracy of genomic prediction exhibited a pattern of initial increase followed by decrease, or continuous decrease across various SNP preselection strategies, as the proportion of selected top SNPs increased. The highest level of prediction accuracy was observed when utilizing 1 or 5% of top SNPs. Compared with the GBLUP model, the utilization of estimated marker effects from a GWAS meta-analysis as SNP weights in the BLUP|GA model improved the accuracy of genomic prediction in different SNP preselection strategies. The new SNP preselection strategies gained from this study bring opportunities for genomic prediction in limited-size populations in pigs.
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Affiliation(s)
- Chen Wei
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Chengjie Chang
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Wenjing Zhang
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Duanyang Ren
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Xiaodian Cai
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Tianru Zhou
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Shaolei Shi
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Xibo Wu
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530022, China; (X.W.); (J.S.)
| | - Jinglei Si
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530022, China; (X.W.); (J.S.)
| | - Xiaolong Yuan
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Jiaqi Li
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
| | - Zhe Zhang
- National Engineering Research Centre for Swine Breeding Industry, Provincial Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510640, China; (C.W.); (C.C.); (W.Z.); (D.R.); (X.C.); (T.Z.); (S.S.); (X.Y.); (J.L.)
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