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Li T, Wan P, Lin Q, Wei C, Guo K, Li X, Lu Y, Zhang Z, Li J. Genome-Wide Association Study Meta-Analysis Elucidates Genetic Structure and Identifies Candidate Genes of Teat Number Traits in Pigs. Int J Mol Sci 2023; 25:451. [PMID: 38203622 PMCID: PMC10779318 DOI: 10.3390/ijms25010451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The teat number is a pivotal reproductive trait that significantly influences the survival rate of piglets. A meta-analysis is a robust instrument, enhancing the universality of research findings and improving statistical power by increasing the sample size. This study aimed to identify universal candidate genes associated with teat number traits using a genome-wide association study (GWAS) meta-analysis with three breeds. We identified 21 chromosome threshold significant single-nucleotide polymorphisms (SNPs) associated with five teat number traits in single-breed and cross-breed meta-GWAS analyses. Using a co-localization analysis of expression quantitative trait loci and GWAS loci, we detected four unique genes that were co-localized with cross-breed GWAS loci associated with teat number traits. Through a meta-analysis and integrative analysis, we identified more reliable candidate genes associated with multiple-breed teat number traits. Our research provides new information for exploring the genetic mechanism affecting pig teat number for breeding selection and improvement.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (T.L.); (P.W.); (Q.L.); (C.W.); (K.G.); (X.L.); (Y.L.); (Z.Z.)
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Ye XW, Gu JM, Cao CY, Zhang ZY, Cheng H, Chen Z, Fang XM, Zhang Z, Wang QS, Pan YC, Wang Z. The jigsaw puzzle of pedigree: whole-genome resequencing reveals genetic diversity and ancestral lineage in Sunong black pigs. Animal 2023; 17:101014. [PMID: 37952495 DOI: 10.1016/j.animal.2023.101014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
The Sunong black pig is a new composite breed under development generated from Chinese indigenous pig breeds (i.e., Taihu and Huai) and intensive pig breeds (i.e., Landrace and Berkshire), which is an important genetic material for studying breeding mechanisms. However, there is currently limited knowledge about the genetic structure and germplasm characteristics of Sunong black pigs. To comprehensively understand their genetic composition and ancestry proportions, we performed population structure and local ancestry inference analysis based on whole-genome sequencing information. The results showed that Sunong black pigs could be clustered independently into a group, whose pedigree was intermediate between indigenous and commercial pig breeds, but closer to commercial pigs. Furthermore, local ancestry inference analysis revealed that Sunong black pigs inherited immune and reproductive traits from indigenous pig breeds, including CC and CXC chemokine family, Toll-like receptor family, IFN gene family, ESR1, AREG and EREG gene, while growth and development-related traits were inherited from commercial pig breeds, including IGF1 and GSY2 gene. Overall, Sunong black pigs have formed a relatively stable genome structure with some advantageous traits inherited from their ancestral breeds. This study deepened the understanding of the breeding mechanism of Sunong black pigs and provided a reference for cross-breeding programmes in livestock.
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Affiliation(s)
- X W Ye
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - J M Gu
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - C Y Cao
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Z Y Zhang
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - H Cheng
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Z Chen
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Str, Nanjing 210014, China
| | - X M Fang
- Institute of Agricultural Product Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Str, Nanjing 210014, China
| | - Z Zhang
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Q S Wang
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Y C Pan
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Z Wang
- College of Animal Sciences, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China.
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Wei C, Cai X, Diao S, Teng J, Xu Z, Zhang W, Zeng H, Zhong Z, Wu X, Gao Y, Li J, Zhang Z. Integrating genome-wide association study with multi-tissue transcriptome analysis provides insights into the genetic architecture of teat traits in pigs. J Genet Genomics 2023; 50:795-798. [PMID: 37453676 DOI: 10.1016/j.jgg.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Chen Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiaodian Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shuqi Diao
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jinyan Teng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zhiting Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Wenjing Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Haonan Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zhanming Zhong
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xibo Wu
- Guangxi State Farms Yongxin Animal Husbandry Group Co. Ltd., Nanning, Guangxi 530022, China
| | - Yahui Gao
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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Gu J, Guo J, Zhang Z, Xu Y, Qadri QR, Zhang Z, Wang Z, Wang Q, Pan Y. Molecular Design-Based Breeding: A Kinship Index-Based Selection Method for Complex Traits in Small Livestock Populations. Genes (Basel) 2023; 14:genes14040807. [PMID: 37107565 PMCID: PMC10137344 DOI: 10.3390/genes14040807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Genomic selection (GS) techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, particularly for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can limit the application of GS in pig breeds with small populations, especially when small populations make up most of the pig breeds worldwide. We aimed to propose a kinship index based selection (KIS) method, which defines an ideal individual with information on the beneficial genotypes for the target trait. Herein, the metric for assessing selection decisions is a beneficial genotypic similarity between the candidate and the ideal individual; thus, the KIS method can overcome the need for establishing genetic reference groups and continuous phenotype determination. We also performed a robustness test to make the method more aligned with reality. Simulation results revealed that compared to conventional genomic selection methods, the KIS method is feasible, particularly, when the population size is relatively small.
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Affiliation(s)
- Jiamin Gu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Jianwei Guo
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
- Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research, Hangzhou 310058, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Qamar Raza Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
- Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research, Hangzhou 310058, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
- Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Correspondence: (Q.W.); (Y.P.)
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
- Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Research, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Correspondence: (Q.W.); (Y.P.)
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