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Zhao Z, Yang Y, Liu P, Yan T, Li R, Pan C, Li Y, Lan X. A Critical Functional Missense Mutation (T117M) in Sheep MC4R Gene Significantly Leads to Gain-of-Function. Animals (Basel) 2024; 14:2207. [PMID: 39123733 PMCID: PMC11311007 DOI: 10.3390/ani14152207] [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: 07/06/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
The melanocortin 4 receptor (MC4R) gene plays a central role in regulating energy homeostasis and food intake in livestock, thereby affecting their economic worth and growth. In a previous study, the p.T117M mutation in the sheep MC4R gene, which leads to the transition of threonine to methionine, was found to affect the body weight at six months and the average daily gain in Hu sheep. However, there are still limited studies on the frequency of the sheep p.T117M missense mutation globally, and the underlying cellular mechanism remains elusive. Therefore, this study first used WGS to investigate the distribution of the MC4R gene p.T117M mutation in 652 individuals across 22 breeds worldwide. The results showed that the mutation frequency was higher in European breeds compared with Chinese sheep breeds, particularly in Poll Dorset sheep (mutation frequency > 0.5). The p.T117M mutation occurs in the first extracellular loop of MC4R. Mechanistically, the basal activity of the mutated receptor is significantly increased. Specifically, upon treatment with α-MSH and ACTH ligands, the cAMP and MAPK/ERK signaling activation of M117 MC4R is enhanced. These results indicate that the T117M mutation may change the function of the gene by increasing the constitutive activity and signaling activation of cAMP and MAPK/ERK, and, thus, may regulate the growth traits of sheep. In conclusion, this study delved into the global distribution and underlying cellular mechanisms of the T117M mutation of the MC4R gene, establishing a scientific foundation for breeding sheep with superior growth, thereby contributing to the advancement of the sheep industry.
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Affiliation(s)
| | | | | | | | | | | | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (Z.Z.); (Y.Y.); (P.L.); (T.Y.); (R.L.); (C.P.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China; (Z.Z.); (Y.Y.); (P.L.); (T.Y.); (R.L.); (C.P.)
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2
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Suárez-Mesa R, Ros-Freixedes R, Pena RN, Reixach J, Estany J. Impact of the leptin receptor gene on pig performance and quality traits. Sci Rep 2024; 14:10652. [PMID: 38730110 PMCID: PMC11087582 DOI: 10.1038/s41598-024-61509-1] [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: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
The recessive T allele of the missense polymorphism rs709596309 C > T of the leptin receptor gene is associated with intramuscular fat. However, its overall impact on pork production is still partial. In this work, we investigated the all-round effects of the TT genotype on lean growth efficiency and carcass, meat and fat quality using data from an experiment that compared the performance of 48 TT and 48 C- (24 CT and 24 CC) Duroc barrows. The TT pigs were less efficient for lean growth than the C- pigs. Although heavier, their carcasses had less lean content, were shorter and had lighter loins. Apart from increasing marbling and saturated fatty acid content, changes caused by the TT genotype in meat and fat quality are likely not enough to be perceived by consumers. The effect on visual marbling score exceeded that on intramuscular fat content, which suggests a direct influence of the T allele on the pattern of fat distribution in muscle. With current low-protein diets, the T allele is expected to be cost-effective only in niche markets where a very high level of marbling is critical.
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Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida - Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida - Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida - Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Josep Reixach
- Selección Batallé S.A., 17421, Riudarenes, Catalonia, Spain
| | - Joan Estany
- Department of Animal Science, University of Lleida - Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
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3
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Suárez-Mesa R, Ros-Freixedes R, Laghouaouta H, Pena RN, Hernández-Ortiz B, Rondón-Barragán I, Estany J. Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing. Trop Anim Health Prod 2023; 55:154. [PMID: 37041265 PMCID: PMC10089996 DOI: 10.1007/s11250-023-03557-9] [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: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
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Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Houda Laghouaouta
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Byron Hernández-Ortiz
- Research and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
| | - Joan Estany
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
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Balatsky VN, Oliinychenko YK, Saienko AM, Buslyk TV, Bankovska IB, Peka MY, Doran O. Associations of Polymorphisms in Leptin and Leptin Receptor Genes with Meat Quality in Pigs of the Ukrainian Large White Breed. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722060020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Li H, Xu C, Meng F, Yao Z, Fan Z, Yang Y, Meng X, Zhan Y, Sun Y, Ma F, Yang J, Yang M, Yang J, Wu Z, Cai G, Zheng E. Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs. Genes (Basel) 2022; 13:2131. [PMID: 36421806 PMCID: PMC9690869 DOI: 10.3390/genes13112131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 07/30/2023] Open
Abstract
The intuitive impression of pork is extremely important in terms of whether consumers are enthusiastic about purchasing it. Flesh color and intramuscular fat (IMF) are indispensable indicators in meat quality assessment. In this study, we determined the flesh color and intramuscular fat at 45 min and 12 h after slaughter (45 mFC, 45 mIMF, 12 hFC, and 12 hIMF) of 1518 commercial Duroc × Landrace × Large White (DLY) pigs. We performed a single nucleotide polymorphism (SNP) genome-wide association study (GWAS) analysis with 28,066 SNPs. This experiment found that the correlation between 45 mFC and 12 hFC was 0.343. The correlation between 45 mIMF and 12 hIMF was 0.238. The heritability of the traits 45 mFC, 12 hFC, 45 mIMF, and 12 hIMF was 0.112, 0.217, 0.139, and 0.178, respectively, and we identified seven SNPs for flesh color and three SNPs for IMF. Finally, several candidate genes regulating these four traits were identified. Three candidate genes related to flesh color were provided: SNCAIP and PRR16 on SSC2, ST3GAL4 on SSC5, and GALR1 on SSC1. A total of three candidate genes related to intramuscular fat were found, including ABLIM3 on SSC2, DPH5 on SSC4, and DOCK10 on SSC15. Furthermore, GO and KEGG analysis revealed that these genes are involved in the regulation of apoptosis and are implicated in functions such as pigmentation and skeletal muscle metabolism. This study applied GWAS to analyze the scoring results of flesh color and IMF in different time periods, and it further revealed the genetic structure of flesh color and IMF traits, which may provide important genetic loci for the subsequent improvement of pig meat quality traits.
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Affiliation(s)
- Hao Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Fanming Meng
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zekai Yao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhenfei Fan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Yingshan Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Xianglun Meng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Yuexin Zhan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ying Sun
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Fucai Ma
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jifei Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
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Estrus Behaviour and Reproductive Traits of Pulawska Gilts Associated with Selected Gene Polymorphisms. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Searching for the associations between the gene polymorphism and the reproductive traits is essential in defining the genetic native breed specificity, which distinguishes them from the other breeds. The aim of our study was to determine the associations between mutations in the PRL, PRLR, PTGS2, FUT1 genes and sexual and periparturient activity in native Pulawska gilts. The analysis included 72 animals which gave birth to the first litter. Evaluation of the productive value of gilts accounted for indicators of sexual and periparturient activity as well as reproductive traits. The biological material for molecular analyses was obtained from the hair roots of the gilts. The genotype was verified by PCR RFLP analysis. The primers and PCR conditions were determined on the basis of available literature data. Statistically significant differences (P≤0.05) were found at the PRL locus: gilts of AA genotypes (Ins/Ins) at the PRL locus were characterised by longest farrowing duration compared to gilts of AB genotype (P≤0.05). The analysis of PRLR gene showed that gilts of TT genotype revealed a tendency for later occurrence of estrus signs (first and second estrus) and for the markedly longest farrowings (P≤0.05). With regard to PTGS2 and FUT1 loci, no significant differences were found in the parameters of sexual and periparturient activity of the gilts. However, gilts of FUT1 GG genotype gave birth to and reared the largest first litters (P≤0.05). The results of the studies expand the knowledge about the genetic structure and productivity of Pulawska gilts.
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7
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Shan H, Song X, Cao Y, Xiong P, Wu J, Jiang J, Jiang Y. Association of the melanocortin 4 receptor (MC4R) gene polymorphism with growth traits of Hu sheep. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Srikanth K, Lee SH, Chung KY, Park JE, Jang GW, Park MR, Kim NY, Kim TH, Chai HH, Park WC, Lim D. A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:E316. [PMID: 32188084 PMCID: PMC7140899 DOI: 10.3390/genes11030316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10-7) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein-protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea;
| | - Ki-Yong Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Mi-Rim Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Na Yeon Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Won Cheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea (J.-E.P.); (G.-W.J.); (M.-R.P.); (N.Y.K.); (T.-H.K.); (H.-H.C.); (W.C.P.)
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Li D, Li F, Jiang K, Zhang M, Han R, Jiang R, Li Z, Tian Y, Yan F, Kang X, Sun G. Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken. PLoS One 2019; 14:e0215006. [PMID: 30964907 PMCID: PMC6456248 DOI: 10.1371/journal.pone.0215006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play important roles in transcriptional and posttranscriptional regulation. However, the effects of lncRNAs on the meat quality of chicken hasn’t been elucidated clearly yet. Gushi chickens are popular in China because of their superior meat quality, particularly the tender flesh, and unique flavor. Gushi chickens are popular in China because of their superior meat quality, delicate flesh, and unique flavor. We performed RNA-Seq analysis of breast muscle from Gushi chicken at two physiological stages, including juvenile (G20W) and laying (G55W). In total, 186 lncRNAs and 881 mRNAs were differentially expressed between G20W and G55W (fold change ≥ 2.0, P < 0.05). Among them, 131 lncRNAs presented upregulated and 55 were downregulated. We identified the cis and trans target genes of the differentially expressed lncRNAs, and constructed lncRNA-mRNA interaction networks. The results showed that differentially expressed mRNAs and lncRNAs were mainly involved in ECM-receptor interaction, glycerophospholipid metabolism, ubiquitin-mediated proteolysis, and the biosynthesis of amino acids. In summary, our study utilized RNA-seq analysis to predict the functions of lncRNA on chicken meat quality. Furthermore, comprehensive analysis identified lncRNAs and their target genes, which may contribute to a better understanding of the molecular mechanisms underlying in poultry meat quality and provide a theoretical basis for further research.
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Affiliation(s)
- Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Keren Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Meng Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
- * E-mail: (GRS); (XTK)
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
- * E-mail: (GRS); (XTK)
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10
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Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, García-Casco J, Alves E, Škrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández AI, Óvilo C. Diversity across major and candidate genes in European local pig breeds. PLoS One 2018; 13:e0207475. [PMID: 30458028 PMCID: PMC6245784 DOI: 10.1371/journal.pone.0207475] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.
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Affiliation(s)
- María Muñoz
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | | | - Fabián García
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Jose M. Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | | | - Joan Tibau
- Programa de Genética y Mejora Animal, IRTA, Barcelona, Spain
| | - Goran Kušec
- University of Osijek, Faculty of Agrobiotechnical Sciences, Osijek, Croatia
| | | | | | - Juliette Riquet
- Génétique Physiologie et Système d’Elevage, INRA, Castanet-Tolosan, France
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Jose P. Araujo
- Instituto Politecnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Čedomir Radović
- Institute for Animal Husbandry-Pig Research Department, Belgrade-Zemun, Serbia
| | - Radomir Savić
- University of Belgrade, Faculty of agriculture, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of animal science, Faculty of agriculture, University of Zagreb, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy
| | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Cristina Óvilo
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
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11
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Association of single nucleotide polymorphisms in leptin (LEP) and leptin receptor (LEPR) genes with backfat thickness and daily weight gain in Ukrainian Large White pigs. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Wang L, Chao Z, Wang Y. Identification of Two Novel Single Nucleotide Polymorphisms in the Promoter Region of the Pig AMP Deaminase 1 Gene Associated with Carcass Traits. DNA Cell Biol 2018; 37:896-902. [PMID: 30234378 DOI: 10.1089/dna.2018.4293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The AMP deaminase 1 (AMPD1) gene plays an important role in purine nucleotide interconversion and energy metabolism. In this study, two novel single nucleotide polymorphisms (SNPs) (g.-626 G > A and g.-566 A>G) were detected in the proximal promoter region of the AMPD1 gene. The Chinese indigenous pig breeds (Meishan and Tongcheng) had higher frequencies of the G and A alleles than Western meat-type breeds (Landrace and Large White) at the g.-626 G > A and g.-566 A>G loci. The transcriptional activity of the AMPD1 promoter carrying the haplotype H1 (A-626G-566) was significantly (p < 0.05) higher than that of the haplotype H2 (G-626A-566). In addition, pigs with the haplotype combination H1H1 had significantly (p < 0.05) higher mRNA expression levels of the AMPD1 gene than those with haplotype combinations H1H2 and H2H2 in two different skeletal muscles. Association analyses revealed that the pigs with the haplotype combination H1H1 had significantly higher lean meat percentage values but lower average backfat thickness (ABT, cm), buttock fat thickness (cm), and thorax-waist fat thickness (cm) values than the pigs with the haplotype combinations H1H2 and H2H2. These findings demonstrate that the two novel SNPs in the promoter region of the AMPD1 gene have significant associations with pig fat deposition traits.
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Affiliation(s)
- Linjie Wang
- 1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, P.R. China
| | - Zhe Chao
- 2 Institute of Animal Science and Veterinary Medicine , Hainan Academy of Agricultural Sciences, Haikou, P.R. China
| | - Yan Wang
- 1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, P.R. China
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13
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A whole-genome sequence based association study on pork eating quality traits and cooking loss in a specially designed heterogeneous F6 pig population. Meat Sci 2018; 146:160-167. [PMID: 30153624 DOI: 10.1016/j.meatsci.2018.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 11/24/2022]
Abstract
To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits.
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14
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Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M, Gurgul A. A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits. Genet Mol Biol 2018; 41:125-136. [PMID: 29658965 PMCID: PMC5901489 DOI: 10.1590/1678-4685-gmb-2016-0101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/11/2017] [Indexed: 12/31/2022] Open
Abstract
Pork is the most popular meat in the world. Unfortunately, the selection pressure
focused on high meat content led to a reduction in pork quality. The present
study used RNA-seq technology to identify metabolic process genes related to
pork quality traits and fat deposition. Differentially expressed genes (DEGs)
were identified between pigs of Pulawska and Polish Landrace breeds for two the
most important muscles (semimembranosus and longissimus
dorsi). A total of 71 significant DEGs were reported: 15 for
longissimus dorsi and 56 for
semimembranosus muscles. The genes overexpressed in
Pulawska pigs were involved in lipid metabolism (APOD,
LXRA, LIPE, AP2B1, ENSSSCG00000028753 and
OAS2) and proteolysis (CST6, CTSD, ISG15
and UCHL1). In Polish Landrace pigs, genes playing a role in
biological adhesion (KIT, VCAN, HES1, SFRP2, CDH11, SSX2IP and
PCDH17), actin cytoskeletal organisation (FRMD6,
LIMK1, KIF23 and CNN1) and calcium ion binding
(PVALB, CIB2, PCDH17, VCAN and CDH11) were
transcriptionally more active. The present study allows for better understanding
of the physiological processes associated with lipid metabolism and muscle fiber
organization. This information could be helpful in further research aiming to
estimate the genetic markers.
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Affiliation(s)
- Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Mirosław Tyra
- Department of Pig Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Artur Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
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15
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Kim JM, Park JE, Lee SW, Cho ES, Choi BH, Park HC, Lee KT, Kim TH. Association of polymorphisms in the 5′ regulatory region of LEPR
gene with meat quality traits in Berkshire pigs. Anim Genet 2017; 48:723-724. [DOI: 10.1111/age.12588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-Mo Kim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
| | - Si-Woo Lee
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
| | - Eun-Seok Cho
- Swine Science Division; National Institute of Animal Science; Rural Development Administration; Cheonan 31000 Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
| | | | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 55365 Korea
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16
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Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens. Sci Rep 2017; 7:45564. [PMID: 28378745 PMCID: PMC5381223 DOI: 10.1038/srep45564] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/27/2017] [Indexed: 01/18/2023] Open
Abstract
Poultry meat quality is associated with breed, age, tissue and other factors. Many previous studies have focused on distinct breeds; however, little is known regarding the epigenetic regulatory mechanisms in different age stages, such as DNA methylation. Here, we compared the global DNA methylation profiles between juvenile (20 weeks old) and later laying-period (55 weeks old) hens and identified candidate genes related to the development and meat quality of breast muscle using whole-genome bisulfite sequencing. The results showed that the later laying-period hens, which had a higher intramuscular fat (IMF) deposition capacity and water holding capacity (WHC) and less tenderness, exhibited higher global DNA methylation levels than the juvenile hens. A total of 2,714 differentially methylated regions were identified in the present study, which corresponded to 378 differentially methylated genes, mainly affecting muscle development, lipid metabolism, and the ageing process. Hypermethylation of the promoters of the genes ABCA1, COL6A1 and GSTT1L and the resulting transcriptional down-regulation in the later laying-period hens may be the reason for the significant difference in the meat quality between the juvenile and later laying-period hens. These findings contribute to a better understanding of epigenetic regulation in the skeletal muscle development and meat quality of chicken.
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17
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Changes in body weight and fatness of sows during reproductive activity depending on LEPR and MC4R genes polymorphism. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Zhang C, Bruce H, Yang T, Charagu P, Kemp RA, Boddicker N, Miar Y, Wang Z, Plastow G. Genome Wide Association Studies (GWAS) Identify QTL on SSC2 and SSC17 Affecting Loin Peak Shear Force in Crossbred Commercial Pigs. PLoS One 2016; 11:e0145082. [PMID: 26901498 PMCID: PMC4763188 DOI: 10.1371/journal.pone.0145082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/27/2015] [Indexed: 01/13/2023] Open
Abstract
Of all the meat quality traits, tenderness is considered the most important with regard to eating quality and market value. In this study we have utilised genome wide association studies (GWAS) for peak shear force (PSF) of loin muscle as a measure of tenderness for 1,976 crossbred commercial pigs, genotyped for 42,721 informative SNPs using the Illumina PorcineSNP60 Beadchip. Four 1 Mb genomic regions, three on SSC2 (at 4 Mb, 5 Mb and 109 Mb) and one on SSC17 (at 20 Mb), were detected which collectively explained about 15.30% and 3.07% of the total genetic and phenotypic variance for PSF respectively. Markers ASGA0008566, ASGA0008695, DRGA0003285 and ASGA0075615 in the four regions were strongly associated with the effects. Analysis of the reference genome sequence in the region with the most important SNPs for SSC2_5 identified FRMD8, SLC25A45 and LTBP3 as potential candidate genes for meat tenderness on the basis of functional annotation of these genes. The region SSC2_109 was close to a previously reported candidate gene CAST; however, the very weak LD between DRGA0003285 (the best marker representing region SSC2_109) and CAST indicated the potential for additional genes which are distinct from, or interact with, CAST to affect meat tenderness. Limited information of known genes in regions SSC2_109 and SSC17_20 restricts further analysis. Re-sequencing of these regions for informative animals may help to resolve the molecular architecture and identify new candidate genes and causative mutations affecting this trait. These findings contribute significantly to our knowledge of the genomic regions affecting pork shear force and will potentially lead to new insights into the molecular mechanisms regulating meat tenderness.
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Affiliation(s)
- Chunyan Zhang
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Heather Bruce
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tianfu Yang
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | | | | | | | - Younes Miar
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
- * E-mail:
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19
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Differential expression of six chicken genes associated with fatness traits in a divergently selected broiler population. Mol Cell Probes 2015; 30:1-5. [PMID: 26746358 DOI: 10.1016/j.mcp.2015.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 12/25/2015] [Accepted: 12/27/2015] [Indexed: 11/24/2022]
Abstract
A genome-wide association study has shown a number of chicken (Gallus gallus) single nucleotide polymorphism (SNP) markers to be significantly associated with abdominal fat content in Northeast Agricultural University (NEAU) broiler lines selected divergently for abdominal fat content (NEAUHLF). The six significant SNPs are located in the kinase insert domain receptor (KDR), tumor suppressor candidate 3 (TUSC3), phosphoribosyl pyrophosphate amidotransferase (PPAT), exocyst complex component 1 (EXOC1), v-myb myeloblastosis viral oncogene homolog (avian)-like 2 (MYBL2) and KIAA1211 (undefined) genes. In this study, the expression levels of these genes were investigated in both abdominal fat and liver tissues using 32 14th generation chickens from the NEAUHLF. The levels of expression of KDR in abdominal fat and KDR and TUSC3 in liver differed significantly between the two lines. The expression level of KDR in the abdominal fat was significantly correlated with the abdominal fat weight (AFW) and abdominal fat percentage (AFP). The expression levels of KDR, TUSC3 and PPAT in liver were significantly correlated with AFW and AFP, indicating that the six genes, especially KDR and TUSC3, could be associated with fat traits in domestic chickens. This study could provide insight into the mechanisms underlying the formation of abdominal fat in chickens.
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20
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Ding YY, Zhang W, Zhang MQ, Fu K, Chen WP, Ding C, He XL, Zhang XD, Huang L, Yin ZJ. Functional and association studies of the cholesteryl ester transfer protein (CETP) gene in a Wannan Black pig model. Anim Genet 2015; 46:702-6. [PMID: 26477338 DOI: 10.1111/age.12370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 10/22/2022]
Abstract
Some polymorphisms of the human CETP gene are causally and significantly associated with serum lipids levels; however, the information regarding this gene in pigs is sparse. To evaluate the effects of CETP on blood lipid traits and fat deposition in pig, porcine CETP tissue expression patterns were observed by quantitative real-time polymerase chain reaction (qPCR) first. High expression was detected in liver, spleen, gluteus medius (GM) muscle and backfat. A de novo polymorphism (AF333037:g.795C>T) in the intron 1 region of porcine CETP was identified. This polymorphism was further genotyped by direct sequencing of the PCR products of 390 Wannan Black pigs, a Chinese native breed population. Association analyses at 45 and 300 days of age revealed highly significant associations between CETP genotypes and serum lipid traits. Furthermore, this polymorphism was proved to be associated with differences in liver CETP mRNA levels: pigs at 300 days of age with the TT genotype had higher levels than did those with other genotypes (P = 0.021). Additionally, analysis at 300 days of age showed that GM CETP mRNA expression correlated positively with serum lipids levels as well as with carcass backfat thickness and intramuscular fat content in GM. These results indicate that CETP is involved in serum, adipose and muscle lipid metabolism in pigs. The mechanisms underlying such relationships and their functional implications are worthy of further research.
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Affiliation(s)
- Y Y Ding
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - W Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - M Q Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - K Fu
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - W P Chen
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - C Ding
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - X L He
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - X D Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - L Huang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - Z J Yin
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
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21
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Zhang C, Wang Z, Bruce H, Kemp RA, Charagu P, Miar Y, Yang T, Plastow G. Genome-wide association studies (GWAS) identify a QTL close to PRKAG3 affecting meat pH and colour in crossbred commercial pigs. BMC Genet 2015; 16:33. [PMID: 25887635 PMCID: PMC4393631 DOI: 10.1186/s12863-015-0192-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 03/23/2015] [Indexed: 12/29/2022] Open
Abstract
Background Improving meat quality is a high priority for the pork industry to satisfy consumers’ preferences. GWAS have become a state-of-the-art approach to genetically improve economically important traits. However, GWAS focused on pork quality are still relatively rare. Results Six genomic regions were shown to affect loin pH and Minolta colour a* and b* on both loin and ham through GWAS in 1943 crossbred commercial pigs. Five of them, located on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, SSC16 and SSCX, were associated with meat colour. However, the most promising region was detected on SSC15 spanning 133–134 Mb which explained 3.51% - 17.06% of genetic variance for five measurements of pH and colour. Three SNPs (ASGA0070625, MARC0083357 and MARC0039273) in very strong LD were considered most likely to account for the effects in this region. ASGA0070625 is located in intron 2 of ZNF142, and the other two markers are close to PRKAG3, STK36, TTLL7 and CDK5R2. After fitting MARC0083357 (the closest SNP to PRKAG3) as a fixed factor, six SNPs still remained significant for at least one trait. Four of them are intragenic with ARPC2, TMBIM1, NRAMP1 and VIL1, while the remaining two are close to RUFY4 and CDK5R2. The gene network constructed demonstrated strong connections of these genes with two major hubs of PRKAG3 and UBC in the super-pathways of cell-to-cell signaling and interaction, cellular function and maintenance. All these pathways play important roles in maintaining the integral architecture and functionality of muscle cells facing the dramatic changes that occur after exsanguination, which is in agreement with the GWAS results found in this study. Conclusions There may be other markers and/or genes in this region besides PRKAG3 that have an important effect on pH and colour. The potential markers and their interactions with PRKAG3 require further investigation Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0192-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunyan Zhang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Heather Bruce
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | | | | | - Younes Miar
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Tianfu Yang
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Graham Plastow
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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