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Yin S, Song G, Gao N, Gao H, Zeng Q, Lu P, Zhang Q, Xu K, He J. Identifying Genetic Architecture of Carcass and Meat Quality Traits in a Ningxiang Indigenous Pig Population. Genes (Basel) 2023; 14:1308. [PMID: 37510213 PMCID: PMC10378861 DOI: 10.3390/genes14071308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Ningxiang pig is a breed renowned for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 min and 24 h) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30~0.80) for carcass traits and from low to high (0.11~0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the GRM4 gene emerged as a pleiotropic gene that correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold the potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Gang Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Hu Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Peng Lu
- Center of Ningxiang Animal Husbandry and Fishery Affairs, Ningxiang 410625, China
| | - Qin Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- College of Animal Science and Technology, China Agricultural University, Beijing 100091, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Chinese Academy of Sciences, The Institute of Subtropical Agriculture, Changsha 410128, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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Oyelami FO, Zhao Q, Xu Z, Zhang Z, Sun H, Zhang Z, Ma P, Wang Q, Pan Y. Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed. Front Genet 2020; 11:752. [PMID: 33101353 PMCID: PMC7498712 DOI: 10.3389/fgene.2020.00752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/23/2020] [Indexed: 11/19/2022] Open
Abstract
The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r2 > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched (p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms (p-value < 0.01), and 2 KEGG pathways (p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyang Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qishan Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China
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Stratz P, Schmid M, Wellmann R, Preuß S, Blaj I, Tetens J, Thaller G, Bennewitz J. Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F 2 crosses. Anim Genet 2018; 49:403-412. [PMID: 29978910 DOI: 10.1111/age.12684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2018] [Indexed: 12/13/2022]
Abstract
In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.
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Affiliation(s)
- P Stratz
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - M Schmid
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - R Wellmann
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - S Preuß
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - I Blaj
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - J Tetens
- Functional Breeding Group, Department of Animal Science, Georg-August-University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - G Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - J Bennewitz
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
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Ponsuksili S, Murani E, Trakooljul N, Schwerin M, Wimmers K. Discovery of candidate genes for muscle traits based on GWAS supported by eQTL-analysis. Int J Biol Sci 2014; 10:327-37. [PMID: 24643240 PMCID: PMC3957088 DOI: 10.7150/ijbs.8134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/22/2014] [Indexed: 12/12/2022] Open
Abstract
Biochemical and biophysical processes that take place in muscle under relaxed and stressed conditions depend on the abundance and activity of gene products of metabolic and structural pathways. In livestock at post-mortem, these muscle properties determine aspects of meat quality and are measurable. The conversion of muscle to meat mimics pathological processes associated with muscle ischemia, injury or damage in humans and it is an economic factor in pork production. Linkage, association, and expression analyses independently contributed to the identification of trait-associated molecular pathways and genes. We aim at providing multiple evidences for the role of specific genes in meat quality by integrating a genome-wide association study (GWAS) for meat quality traits and the detection of eQTL based on trait-correlated expressed genes and trait-associated markers. The GWAS revealed 51 and 200 SNPs significantly associated with meat quality in a crossbred Pietrain×(German Landrace×Large White) (Pi×(GL×LW)) and a purebred German Landrace (GL) population, respectively. Most significant SNPs in Pi×(GL×LW) were located on chromosomes (SSC) 4 and 6. The data of 47,836 eQTLs at a significance level of p<10-5 were used to scale down the number candidate genes located in these regions. These SNPs on SSC4 showed association with expression levels of ZNF704, IMPA1, and OXSR1; SSC6 SNPs were associated with expression of SIGLEC10 and PIH1D1. Most significant SNPs in GL were located on SSC6 and associated with expression levels of PIH1D1, SIGLEC10, TBCB, LOC100518735, KIF1B, LOC100514845, and two unknown genes. The abundance of transcripts of these genes in muscle, in turn, is significantly correlated with meat quality traits. We identified several genes with evidence for their candidacy for meat quality arising from the integrative approach of a genome-wide association study and eQTL analysis.
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Affiliation(s)
- Siriluck Ponsuksili
- 1. Research Group 'Functional Genome Analyses', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Eduard Murani
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Nares Trakooljul
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Manfred Schwerin
- 1. Research Group 'Functional Genome Analyses', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Klaus Wimmers
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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Stratz P, Wellmann R, Preuss S, Wimmers K, Bennewitz J. Genome-wide association analysis for growth, muscularity and meat quality in Piétrain pigs. Anim Genet 2014; 45:350-6. [DOI: 10.1111/age.12133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2013] [Indexed: 12/21/2022]
Affiliation(s)
- P. Stratz
- Institute of Animal Husbandry and Breeding; University of Hohenheim; D-70599 Stuttgart Germany
| | - R. Wellmann
- Institute of Animal Husbandry and Breeding; University of Hohenheim; D-70599 Stuttgart Germany
| | - S. Preuss
- Institute of Animal Husbandry and Breeding; University of Hohenheim; D-70599 Stuttgart Germany
| | - K. Wimmers
- Research Unit Molecular Biology; Institute for Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); Wilhelm-Stahl-Allee 2 D-18196 Dummerstorf Germany
| | - J. Bennewitz
- Institute of Animal Husbandry and Breeding; University of Hohenheim; D-70599 Stuttgart Germany
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