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Ke J, Chen C, Fei J, Luo K, Cheng Y, Yu H, Cheng C, Yan Y, Zhang X, Liang S, Sun H, Bai C, Sun B. Genome-wide analysis of genetic loci and candidate genes related to teat number traits in Dongliao black pigs. Front Genet 2025; 16:1593395. [PMID: 40438329 PMCID: PMC12116542 DOI: 10.3389/fgene.2025.1593395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Accepted: 04/29/2025] [Indexed: 06/01/2025] Open
Abstract
This study investigated the genetic basis of teat number variation in Dongliao black pigs. A total of 765 pigs were genotyped using the Porcine 50K SNP chip, and their teat numbers were recorded. Heritability estimates for total teat number (TTN) and teat pair number (TPN) were 0.091 and 0.097, respectively. Genome-wide association studies identified 74 significant SNPs for TTN and 105 for TPN. Nine candidate genes related to the teat number were identified: CSNK1G1, PLEKHM2, CABLES1, SLC25A21, RYR3, PIGH, GUCY1A1, RAPGEF2, and TRPC4AP. These findings provide insights into the genetic architecture of teat number variation in Dongliao black pigs.
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Affiliation(s)
- Juan Ke
- College of Animal Science, Jilin University, Changchun, China
| | - Changyi Chen
- College of Animal Science, Jilin University, Changchun, China
| | - Junwen Fei
- College of Animal Science, Jilin University, Changchun, China
| | - Ke Luo
- College of Animal Science, Jilin University, Changchun, China
| | - Yu Cheng
- College of Animal Science, Jilin University, Changchun, China
| | - Huimin Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Chao Cheng
- Jilin Shuangtian Ecological Agriculture Co., LTD., Liaoyuan, China
| | - Yiqing Yan
- College of Animal Science, Jilin University, Changchun, China
| | - Xiaoran Zhang
- College of Animal Science, Jilin University, Changchun, China
| | - Shuang Liang
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Chunyan Bai
- College of Animal Science, Jilin University, Changchun, China
| | - Boxing Sun
- College of Animal Science, Jilin University, Changchun, China
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Tao L, Liu H, Adeola AC, Xie HB, Feng ST, Zhang YP. The effects of runs-of-homozygosity on pig domestication and breeding. BMC Genomics 2025; 26:6. [PMID: 39762732 PMCID: PMC11702194 DOI: 10.1186/s12864-024-11189-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 12/27/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression. RESULTS Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data. CONCLUSIONS These findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Liu
- Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Adeniyi C Adeola
- Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hai-Bing Xie
- Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shu-Tang Feng
- Beijing Grand-Life Science and Technology Company, Beijing, 102206, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ya-Ping Zhang
- Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Science, Yunnan University, Kunming, 650091, China.
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Qiu Z, Yin Y, Huang R, Zhou J, Liu Q, Liu K, Liu C, Li P, Zhao Q. Multiple association studies identify 3 novel candidate genes for teat number trait in Danish Landrace and Large White pigs: BRINP3, LIN52, and UBE3B. J Anim Sci 2025; 103:skaf145. [PMID: 40305433 PMCID: PMC12124257 DOI: 10.1093/jas/skaf145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Accepted: 04/24/2025] [Indexed: 05/02/2025] Open
Abstract
Milk is an essential source of nutrition for preweaning piglets. Therefore, in the breeding process, sows were expected to have sufficient teats to suckle their piglets. However, in Danish Landrace and Large White pigs, the number of piglets born currently exceeds the number of teats, making it urgent to select and breed for an increased teat number. In this study, the samples of 491 Danish Landrace pigs and 1,047 Danish Large White pigs with teat number phenotype were used to perform genome-wide association studies to identify SNPs associated with total teat number (TTN) based on SNP-chip data and data imputed to the level of whole-genome sequencing (iWGS), respectively. In Landrace pigs, the most significant SNP on SSC10 explains 5.14% of the phenotypic variance, while in Large White pigs, the most significant SNP on SSC7 explains 4.46% of the phenotypic variance. Additionally, linkage disequilibrium and linkage analysis (LDLA) were used to refine the regions of QTLs on SSC10 to 2.89 to 5.43 Mb in Danish Landrace pigs and to 96.00 to 97.95 Mb on SSC7 in Danish Large White pigs, respectively. To maximize the utility of information from 2 populations, meta-analysis was conducted across multiple populations. A total of 12 protein-coding genes were identified within the candidate QTL regions determined by LDLA and meta-analysis. To supplement the candidate gene set, transcriptome-wide association studies (TWAS) based on embryo and placenta tissues identified 7 protein-coding genes associated with TTN in Landrace and Large White pigs. Phenome-wide association studies (PheWAS) query was conducted for all the above genes, revealing that nearly all of them are associated with teat number traits. Additionally, some genes showed strong associations with carcass traits, suggesting a potential association between teat number and carcass traits. Through functional annotation and integrated analysis, BRINP3, LIN52, ABCD4, and UBE3B were determined as the functional candidate genes regulating TTN. These findings lay the foundation for identifying the genetic loci regulating teat number in Danish pigs, as well as for their molecular breeding.
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Affiliation(s)
- Zijian Qiu
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Yanzhen Yin
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Ruihua Huang
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Animal Science & Technology, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Jin Zhou
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Qian Liu
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Kaiyue Liu
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Chenxi Liu
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Pinghua Li
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Animal Science & Technology, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Qingbo Zhao
- Key Laboratory (Nanjing) for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Animal Science & Technology, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
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