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Nonneman DJ, Lents CA. Functional genomics of reproduction in pigs: Are we there yet? Mol Reprod Dev 2023; 90:436-444. [PMID: 35704517 DOI: 10.1002/mrd.23625] [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: 03/01/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.
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Affiliation(s)
- Dan J Nonneman
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Clay A Lents
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
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Yin Y, Hou L, Liu C, Li K, Guo H, Niu P, Li Q, Huang R, Li P. Genome-Wide Association Study Identified a Quantitative Trait Locus and Two Candidate Genes on Sus scrofa Chromosome 2 Affecting Vulvar Traits of Suhuai Pigs. Genes (Basel) 2022; 13:genes13081294. [PMID: 35893031 PMCID: PMC9330916 DOI: 10.3390/genes13081294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Vulvar size and angle are meaningful traits in pig production. Sows with abnormal vulva generally show reproductive disorders. In order to excavate candidate loci and genes associated with pig’s vulvar traits, 270 Suhuai pigs with vulvar phenotype were genotyped by a porcine single nucleotide polymorphisms (SNP) Chip. Then, Chip data were imputed using resequenced data of 30 Suhuai pigs as a reference panel. Next, we estimated the heritability and performed a genome-wide association study (GWAS) for vulvar traits. The heritabilities for the traits vulvar length (VL), vulvar width (VW) and vulvar angle (VA) in this pig population were 0.23, 0.32 and 0.22, respectively. GWAS based on Chip data identified nine significant SNPs on the Sus scrofa chromosomes (SSC) 2, 7, 9 and 13 for VL or VW. GWAS based on imputed data identified 11 new quantitative trait loci (QTL) on SSC1, 2, 7, 8, 9, 11, 13, 16 and 17 for VL or VW. The most significant QTL for VL on SSC2 were refined to a 3.48–3.97 Mb region using linkage disequilibrium and linkage analysis (LDLA). In this refined region, FGF19 and CCND1, involved in the development of the reproductive tract, cell growth and vulvar cancer, could be new candidate genes affecting VL. Our results provided potential genetic markers for the breeding of vulvar traits in pigs and deepened the understanding of the genetic mechanism of vulvar traits.
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Affiliation(s)
- Yanzhen Yin
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
| | - Liming Hou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China;
| | - Chenxi Liu
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijun Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Guo
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China;
| | - Qiang Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China;
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China;
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.H.); (C.L.); (K.L.); (H.G.); (R.H.)
- Key Laboratory in Nanjing for Evaluation and Utilization of Livestock and Poultry (Pigs) Resources, Ministry of Agriculture and Rural Areas, Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China;
- Correspondence:
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Xu W, Wang Z, Qu Y, Li Q, Tian Y, Chen L, Tang J, Li C, Li G, Shen J, Tao Z, Cao Y, Zeng T, Lu L. Genome-Wide Association Studies and Haplotype-Sharing Analysis Targeting the Egg Production Traits in Shaoxing Duck. Front Genet 2022; 13:828884. [PMID: 35419032 PMCID: PMC8995972 DOI: 10.3389/fgene.2022.828884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Age at first egg (AFE) and egg number (EN) are economically important traits related to egg production, as they directly influence the benefits of the poultry industry, but the molecular genetic research that affects those traits in laying ducks is still sparse. Our objective was to identify the genomic regions and candidate genes associated with AFE, egg production at 43 weeks (EP43w), and egg production at 66 weeks (EP66w) in a Shaoxing duck population using genome-wide association studies (GWASs) and haplotype-sharing analysis. Single-nucleotide polymorphism (SNP)-based genetic parameter estimates showed that the heritability was 0.15, 0.20, and 0.22 for AFE, EP43w, and EP66w, respectively. Subsequently, three univariate GWASs for AFE, EP43w, and EP66w were carried out independently. Twenty-four SNPs located on chromosome 25 within a 0.01-Mb region that spans from 4.511 to 4.521 Mb were associated with AFE. There are two CIs that affect EP43w, i.e., twenty-five SNPs were in strong linkage disequilibrium region spanning from 3.186 to 3.247 Mb on chromosome 25, a region spanning from 4.442 to 4.446 Mb on chromosome 25, and two interesting genes, ACAD8 and THYN1, that may affect EP43w in laying ducks. There are also two CIs that affect EP66w, i.e., a 2.412-Mb region that spans from 127.497 to 129.910 Mb on chromosome 2 and a 0.355-Mb region that spans from 4.481 to 4.837 Mb on chromosome 29, and CA2 and GAMT may be the putative candidate genes. Our study also found some haplotypes significantly associated with these three traits based on haplotype-sharing analysis. Overall, this study was the first publication of GWAS on egg production in laying ducks, and our findings will be helpful to provide some candidate genes and haplotypes to improve egg production performance based on breeding in laying duck. Additionally, we learned from a method called bootstrap test to verify the reliability of a GWAS with small experimental samples that users can access at https://github.com/xuwenwu24/Bootstrap-test.
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Affiliation(s)
- Wenwu Xu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenzhen Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuanqi Qu
- Hubei Shendan Co., Ltd., Wuhan, China
| | - Qingyi Li
- Hubei Shendan Co., Ltd., Wuhan, China
| | - Yong Tian
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | | | - Guoqin Li
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junda Shen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhengrong Tao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yongqing Cao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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