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Zhang M, Zha X, Ma X, La Y, Guo X, Chu M, Bao P, Yan P, Wu X, Liang C. Genome-Wide Transcriptome Profiling Reveals the Mechanisms Underlying Hepatic Metabolism under Different Raising Systems in Yak. Animals (Basel) 2024; 14:695. [PMID: 38473080 DOI: 10.3390/ani14050695] [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: 12/20/2023] [Revised: 02/10/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Yak meat is nutritionally superior to beef cattle but has a low fat content and is slow-growing. The liver plays a crucial role in lipid metabolism, and in order to determine whether different feeding modes affect lipid metabolism in yaks and how it is regulated, we employed RNA sequencing (RNA-seq) technology to analyze the genome-wide differential gene expression in the liver of yaks maintained under different raising systems. A total of 1663 differentially expressed genes (DEGs) were identified (|log2FC| ≥ 0 and p-value ≤ 0.05), including 698 down-regulated and 965 up-regulated genes. According to gene ontology (GO) and KEGG enrichment analyses, these DEGs were significantly enriched in 13 GO terms and 26 pathways (p < 0.05). Some DEGs were enriched in fatty acid degradation, PPAR, PI3K-Akt, and ECM receptor pathways, which are associated with lipid metabolism. A total of 16 genes are well known to be related to lipid metabolism (e.g., APOA1, FABP1, EHHADH, FADS2, SLC27A5, ACADM, CPT1B, ACOX2, HMGCS2, PLIN5, ACAA1, IGF1, FGFR4, ALDH9A1, ECHS1, LAMA2). A total of 11 of the above genes were significantly enriched in the PPAR signaling pathway. The reliability of the transcriptomic data was verified using qRT-PCR. Our findings provide new insights into the mechanisms regulating yak meat quality. It shows that fattening improves the expression of genes that regulate lipid deposition in yaks and enhances meat quality. This finding will contribute to a better understanding of the various factors that determine yak meat quality and help develop strategies to improve yield and quality.
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Affiliation(s)
- Mengfan Zhang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xita Zha
- Qinghai Province Qilian County Animal Husbandry and Veterinary Workstation, Qilian 810400, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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Cho E, Kim M, Cho S, So HJ, Lee KT, Cha J, Jin D, Lee JH. A genome-wide association study for the fatty acid composition of breast meat in an F2 crossbred chicken population. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:735-747. [PMID: 37970507 PMCID: PMC10640945 DOI: 10.5187/jast.2023.e1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 11/17/2023]
Abstract
The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published. The majority of these studies focused on pigs and cattle; the association between fatty acid composition and meat quality in chickens has rarely been reported. Therefore, this study investigated candidate genes associated with fatty acid composition in chickens. A genome-wide association study (GWAS) was performed on 767 individuals from an F2 crossbred population of Yeonsan Ogye and White Leghorn chickens. The Illumina chicken 60K significant single-nucleotide polymorphism (SNP) genotype data and 30 fatty acids (%) in the breast meat of animals slaughtered at 10 weeks of age were analyzed. SNPs were shown to be significant in 15 traits: C10:0, C14:0, C18:0, C18:1n-7, C18:1n-9, C18:2n-6, C20:0, C20:2, C20:3n-6, C20:4n-6, C20:5n-3, C24:0, C24:1n-9, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). These SNPs were mostly located on chromosome 10 and around the following genes: ACSS3, BTG1, MCEE, PPARGC1A, ACSL4, ELOVL4, CYB5R4, ME1, and TRPM1. Both oleic acid and arachidonic acid contained the candidate genes: MCEE and TRPM1. These two fatty acids are antagonistic to each other and have been identified as traits that contribute to the production of volatile fatty acids. The results of this study improve our understanding of the genetic mechanisms through which fatty acids in chicken affect the meat flavor.
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Affiliation(s)
- Eunjin Cho
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
| | - Minjun Kim
- Division of Animal & Dairy Science,
Chungnam National University, Daejeon 34134, Korea
| | - Sunghyun Cho
- Research and Development Center,
Insilicogen Inc., Yongin 19654, Korea
| | - Hee-Jin So
- Department of Food Science and Technology,
Chungnam National University, Daejeon 34134, Korea
| | - Ki-Teak Lee
- Department of Food Science and Technology,
Chungnam National University, Daejeon 34134, Korea
| | - Jihye Cha
- Animal Genome & Bioinformatics,
National Institute of Animal Science, Rural Development
Administration, Wanju 55365, Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center,
National Institute of Animal Science, Rural Development
Administration, Hamyang 50000, Korea
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
- Division of Animal & Dairy Science,
Chungnam National University, Daejeon 34134, Korea
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3
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Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq. Sci Rep 2023; 13:535. [PMID: 36631502 PMCID: PMC9834388 DOI: 10.1038/s41598-022-27016-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candidate genes, biological processes, and pathways involved in the modulation of intramuscular FA profile from longissimus dorsi muscle. FA profile by gas chromatography of methyl esters and gene expression by RNA-Seq were determined in 129 Iberian × Duroc backcrossed pigs. An association analysis between the muscle transcriptome and its FA profile was performed, followed by a concordance and functional analysis. Overall, a list of well-known (e.g., PLIN1, LEP, ELOVL6, SC5D, NCOA2, ACSL1, MDH1, LPL, LGALS12, TFRC, GOT1, and FBP1) and novel (e.g., TRARG1, TANK, ENSSSCG00000011196, and ENSSSCG00000038429) candidate genes was identified, either in association with specific or several FA traits. Likewise, several of these genes belong to biological processes and pathways linked to energy, lipid, and carbohydrate metabolism, which seem determinants in the modulation of FA compositions. This study can contribute to elucidate the complex relationship between gene expression and FA profile in pig muscle.
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RNA-Seq Analysis Identifies Differentially Expressed Genes in the Longissimus dorsi of Wagyu and Chinese Red Steppe Cattle. Int J Mol Sci 2022; 24:ijms24010387. [PMID: 36613828 PMCID: PMC9820533 DOI: 10.3390/ijms24010387] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
Meat quality has a close relationship with fat and connective tissue; therefore, screening and identifying functional genes related to lipid metabolism is essential for the production of high-grade beef. The transcriptomes of the Longissimus dorsi muscle in Wagyu and Chinese Red Steppe cattle, breeds with significant differences in meat quality and intramuscular fat deposition, were analyzed using RNA-seq to screen for candidate genes associated with beef quality traits. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the 388 differentially expressed genes (DEGs) were involved in biological processes such as short-chain fatty acid metabolism, regulation of fatty acid transport and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In addition, crystallin alpha B (CRYAB), ankyrin repeat domain 2 (ANKRD2), aldehyde dehydrogenase 9 family member A1 (ALDH9A1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) were investigated for their effects on intracellular triglyceride and fatty acid content and their regulatory effects on genes in lipogenesis and fatty acid metabolism pathways. This study generated a dataset from transcriptome profiling of two cattle breeds, with differing capacities for fat-deposition in the muscle, and revealed molecular evidence that CRYAB, ANKRD2, ALDH9A1 and EHHADH are related to fat metabolism in bovine fetal fibroblasts (BFFs). The results provide potential functional genes for maker-assisted selection and molecular breeding to improve meat quality traits in beef cattle.
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Mekchay S, Pothakam N, Norseeda W, Supakankul P, Teltathum T, Liu G, Naraballobh W, Khamlor T, Sringarm K, Krutmuang P. Association of IFNA16 and TNFRSF19 Polymorphisms with Intramuscular Fat Content and Fatty Acid Composition in Pigs. BIOLOGY 2022; 11:109. [PMID: 35053107 PMCID: PMC8773020 DOI: 10.3390/biology11010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Interferon-alpha-16 (IFNA16) and tumor necrosis factor receptor superfamily member 19 (TNFRSF19) are cytokines that may play a role in adipogenesis and fatness. Single nucleotide polymorphisms (SNPs) of the porcine IFNA16 and TNFRSF19 genes were verified and their association with intramuscular fat (IMF) content and fatty acid (FA) composition were evaluated in commercial crossbred pigs. Two non-synonymous SNPs of the porcine IFNA16 c.413G > A and TNFRSF19 c.860G > C loci were detected in commercial crossbred pigs. The porcine IFNA16 c.413G >A polymorphism was significantly associated with stearic acid, total saturated FAs (SFAs), and the ratio of monounsaturated FAs (MUFAs) to SFAs (p < 0.05). Furthermore, the porcine TNFRSF19 c.860G > C polymorphism was found to be significantly associated with IMF content and arachidic acid levels (p < 0.05). The results revealed that porcine IFNA16 and TNFRSF19 polymorphisms are related to IMF content and/or FA composition and affirmed the importance of these cytokine genes as potential candidate genes for lipid deposition and FA composition in the muscle tissue of pigs.
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Affiliation(s)
- Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Nanthana Pothakam
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand
- Veterinary, Conservation and Research Section, Animal Management Division, Chiang Mai Night Safari, Chiang Mai 50230, Thailand
| | - Worrarak Norseeda
- Department of Agriculture, Faculty of Agricultural Technology, Lampang Rajabhat University, Lampang 52100, Thailand;
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand;
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand;
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Patcharin Krutmuang
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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Blay C, Haffray P, D'Ambrosio J, Prado E, Dechamp N, Nazabal V, Bugeon J, Enez F, Causeur D, Eklouh-Molinier C, Petit V, Phocas F, Corraze G, Dupont-Nivet M. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. BMC Genomics 2021; 22:788. [PMID: 34732127 PMCID: PMC8564959 DOI: 10.1186/s12864-021-08062-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection. Results Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait. Conclusion This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08062-7.
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Affiliation(s)
- Carole Blay
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Jonathan D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,SYSAAF, Station LPGP-INRAE, Rennes, France
| | - Enora Prado
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | - Nicolas Dechamp
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Virginie Nazabal
- University of Rennes, CNRS, ISCR - UMR 6226, ScanMAT - UMS 2001, Rennes, France
| | | | | | - David Causeur
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, Rennes, France
| | | | | | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Geneviève Corraze
- INRAE, University of Pau & Pays Adour, E2S UPPA, UMR1419 NuMéA, St Pée sur, Nivelle, France
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Yan G, Liu X, Xiao S, Xin W, Xu W, Li Y, Huang T, Qin J, Xie L, Ma J, Zhang Z, Huang L. An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population. SCIENCE CHINA-LIFE SCIENCES 2021; 65:781-794. [PMID: 34387836 DOI: 10.1007/s11427-020-1960-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/19/2021] [Indexed: 01/08/2023]
Abstract
Sequencing-based genome-wide association studies (GWAS) have facilitated the identification of causal associations between genetic variants and traits in diverse species. However, it is cost-prohibitive for the majority of research groups to sequence a large number of samples. Here, we carried out genotype imputation to increase the density of single nucleotide polymorphisms in a large-scale Swine F2 population using a reference panel including 117 individuals, followed by a series of GWAS analyses. The imputation accuracies reached 0.89 and 0.86 for allelic concordance and correlation, respectively. A quantitative trait nucleotide (QTN) affecting the chest vertebrate was detected directly, while the investigation of another QTN affecting the residual glucose failed due to the presence of similar haplotypes carrying wild-type and mutant allelesin the reference panel used in this study. A high imputation accuracy was confirmed by Sanger sequencing technology for the most significant loci. Two candidate genes, CPNE5 and MYH3, affecting meat-related traits were proposed. Collectively, we illustrated four scenarios in imputation-based GWAS that may be encountered by researchers, and our results will provide an extensive reference for future genotype imputation-based GWAS analyses in the future.
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Affiliation(s)
- Guorong Yan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xianxian Liu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenshui Xin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenwu Xu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yiping Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiangtao Qin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Xie
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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Pothakam N, Supakankul P, Norseeda W, Liu G, Teltathum T, Naraballobh W, Khamlor T, Sringarm K, Mekchay S. Association of adipocytokine IL-1A and IL-6 genes with intramuscular fat content and fatty acid composition in pigs. Meat Sci 2021; 179:108554. [PMID: 34000609 DOI: 10.1016/j.meatsci.2021.108554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/22/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
Several adipocytokines are involved in inflammatory and immune responses as well as regulated fat deposition and lipid metabolism in mammals. This study aimed to verify the polymorphisms of the porcine interleukin 1A (IL-1A) and interleukin 6 (IL-6) genes and to assess their association with intramuscular fat (IMF) content and fatty acid (FA) composition in commercial crossbred pigs. Two single nucleotide polymorphisms (SNPs) of the porcine IL-1A g.43722547A>G and IL-6 g.91508173C>T loci were found to be segregating in these crossbred pigs. Furthermore, the porcine IL-1A g.43722547A>G polymorphism was found to be significantly associated with myristic, palmitic, palmitoleic, and eicosadienoic acid levels. Moreover, the porcine IL-6 g.91508173C>T polymorphism was significantly associated with IMF content and homolinolenic acid levels. These results suggest that the polymorphisms of the porcine IL-1A and IL-6 genes correlated with lipid content and FA composition and confirmed the importance of the adipocytokine IL-1A and IL-6 genes as candidate genes for fatty acid composition in the muscles of pigs.
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Affiliation(s)
- Nanthana Pothakam
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Worrarak Norseeda
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand.
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Zhou S, Ding R, Meng F, Wang X, Zhuang Z, Quan J, Geng Q, Wu J, Zheng E, Wu Z, Yang J, Yang J. A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations. BMC Genomics 2021; 22:12. [PMID: 33407097 PMCID: PMC7788875 DOI: 10.1186/s12864-020-07288-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.
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Affiliation(s)
- Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of 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, Guangdong, People's Republic of China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qian Geng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jianhui Yang
- YueYang Vocational Technical College, Yueyang, 414000, Hunan, People's Republic of China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
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10
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Mihelic R, Winter H, Powers JB, Das S, Lamour K, Campagna SR, Voy BH. Genes controlling polyunsaturated fatty acid synthesis are developmentally regulated in broiler chicks. Br Poult Sci 2020; 61:508-517. [PMID: 32316746 DOI: 10.1080/00071668.2020.1759788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
1. The objective of this study was to characterise the regulation of the pathways that synthesise long-chain polyunsaturated fatty acids (PUFA) on developing adipose deposits in broiler embryos and chicks. Subcutaneous adipose depots were harvested from embryos and embryonic d E13, E15 and E17. Subcutaneous, abdominal and crop (neck) adipose, as well as liver, were collected at 7 and 14 d post-hatch. 2. Targeted RNA sequencing was used to quantify expression of 6 elongation of very long-chain fatty acid (ELOVL) genes, two isoforms of stearoyl-CoA desaturase (SCD and SCD5), and three fatty acid desaturases (FADS1, FADS2, and FADS6) in each depot and in the liver. Expression levels of marker genes for fatty acid oxidation and adipogenesis (peroxisome proliferator-activated receptor gamma (PPARG)) were quantified. Fatty acid composition of subcutaneous adipose was analysed using gas chromatograph-mass spectrometry (GC/MS). 3. Genes in the PUFA synthetic pathway were differentially expressed across developmental ages and between depots. These include elongase and desaturase genes, that have not previously been characterised in chicken. Correlation analyses identified subsets of co-regulated genes and fatty acids and highlighted relationships that may influence adipose metabolism and development. 4. It was concluded that PUFA synthesis is an active and dynamically regulated pathway in developing adipose deposits in the broiler chick. These data highlighted potential novel roles for specific elongase and desaturase genes in adipose deposition and metabolism.
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Affiliation(s)
- R Mihelic
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - H Winter
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - J B Powers
- Department of Chemistry, University of Tennessee , Knoxville, TN, USA.,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee , Knoxville, TN, USA
| | - S Das
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN, USA
| | - S R Campagna
- Department of Chemistry, University of Tennessee , Knoxville, TN, USA.,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee , Knoxville, TN, USA
| | - B H Voy
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
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11
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Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig. Sci Rep 2020; 10:13962. [PMID: 32811870 PMCID: PMC7435270 DOI: 10.1038/s41598-020-70894-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.
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12
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Criado-Mesas L, Ballester M, Crespo-Piazuelo D, Castelló A, Fernández AI, Folch JM. Identification of eQTLs associated with lipid metabolism in Longissimus dorsi muscle of pigs with different genetic backgrounds. Sci Rep 2020; 10:9845. [PMID: 32555447 PMCID: PMC7300017 DOI: 10.1038/s41598-020-67015-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten Sus scrofa regions and associated with the expression of ACSM5, ACSS2, ATF3, DGAT2, FOS and IGF2 (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for IGF2 and ACSM5 were classified as cis-acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed trans-regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common trans-eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.
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Affiliation(s)
- Lourdes Criado-Mesas
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain.
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca y Tecnologia Agraroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Anna Castelló
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Josep M Folch
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
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13
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Ropka-Molik K, Pawlina-Tyszko K, Żukowski K, Tyra M, Derebecka N, Wesoły J, Szmatoła T, Piórkowska K. Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels. Genes (Basel) 2020; 11:E600. [PMID: 32485856 PMCID: PMC7348756 DOI: 10.3390/genes11060600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/29/2022] Open
Abstract
Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Mirosław Tyra
- Department of Pig Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Uniwersytetu Poznanskiego street 6, 61-614 Poznań, Poland; (N.D.); (J.W.)
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Uniwersytetu Poznanskiego street 6, 61-614 Poznań, Poland; (N.D.); (J.W.)
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
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14
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Genome-wide association study identifies quantitative trait loci regions involved in muscle acidic profile in Large White heavy pigs. Animal 2020; 14:1342-1350. [PMID: 32037995 DOI: 10.1017/s1751731120000099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic : palmitic and oleic : stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E-07). Of particular interest, the palmitoleic : palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products.
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15
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Zhang J, Zhang Y, Gong H, Cui L, Ma J, Chen C, Ai H, Xiao S, Huang L, Yang B. Landscape of Loci and Candidate Genes for Muscle Fatty Acid Composition in Pigs Revealed by Multiple Population Association Analysis. Front Genet 2019; 10:1067. [PMID: 31708975 PMCID: PMC6824322 DOI: 10.3389/fgene.2019.01067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/04/2019] [Indexed: 01/19/2023] Open
Abstract
Genome wide association analyses in diverse populations can identify complex trait loci that are specifically present in one population or shared across multiple populations, which help to better understand the genetic architecture of complex traits in a broader genetic context. In this study, we conducted genome-wide association studies and meta-analysis for 38 fatty acid composition traits with 12–19 million imputed genome sequence SNPs in 2446 pigs from six populations, encompassing White Duroc × Erhualian F2, Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian, and Bamaxiang pigs that were originally genotyped with 60 K or 1.4 million single nucleotide polymorphism (SNP) chips. The analyses uncovered 285 lead SNPs (P < 5 × 10-8), among which 78 locate more than 1 Mb to the lead chip SNPs were considered as novel, largely augmented the landscape of loci for porcine muscle fatty acid composition. Meta-analysis enhanced the association significance at loci near FADS2, ABCD2, ELOVL5, ELOVL6, ELOVL7, SCD, and THRSP genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at SCD loci identified a shared 3.7 kb haplotype in F2, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at FASN loci, we found an Erhualian specific haplotype explaining the population specific association signals in Erhualian pigs. This study refines our understanding on landscape of loci and candidate genes for fatty acid composition traits of pigs.
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Affiliation(s)
- Junjie Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yifeng Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Leilei Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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16
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Zhang Y, Zhang J, Gong H, Cui L, Zhang W, Ma J, Chen C, Ai H, Xiao S, Huang L, Yang B. Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations. Meat Sci 2019; 150:47-55. [DOI: 10.1016/j.meatsci.2018.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
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17
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Wang Z, Zhu B, Niu H, Zhang W, Xu L, Xu L, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle. J Anim Sci Biotechnol 2019; 10:27. [PMID: 30867906 PMCID: PMC6399853 DOI: 10.1186/s40104-019-0322-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/14/2019] [Indexed: 12/29/2022] Open
Abstract
Background Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle. Results In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B). Conclusions Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.
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Affiliation(s)
- Zezhao Wang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.,2National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Bo Zhu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hong Niu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Wengang Zhang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ling Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lei Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.,3Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Yan Chen
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lupei Zhang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xue Gao
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Huijiang Gao
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Shengli Zhang
- 2National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Lingyang Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Junya Li
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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18
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González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M. Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles. BMC Genomics 2019; 20:170. [PMID: 30832586 PMCID: PMC6399881 DOI: 10.1186/s12864-019-5557-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. RESULTS A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110-114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. CONCLUSIONS We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramona N. Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, 25198 Lleida, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF 70.040-020 Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 Canada
| | - Isabel Díaz
- Institute for Research and Technology in Food and Agriculture (IRTA), Tecnologia dels Aliments, 17121 Monells, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Association study highlights the influence of ELOVL fatty acid elongase 6 gene region on backfat fatty acid composition in Large White pig breed. Animal 2018; 12:2443-2452. [PMID: 29580300 DOI: 10.1017/s1751731118000484] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dietary fatty acid (FA) composition has an impact on human health. There is an increasing request from consumers for healthier food and pork industry must respond to it without worsening performance and the technological properties of pork products. The inclusion of genetic markers for carcass FA composition in pig selection schemes could be a useful tool to reach the right balance between unsaturated and saturated FAs to satisfy market demands. With the aim of finding genomic regions associated with porcine backfat FA composition, a genome-wide association study was performed on 798 Italian Large White pigs genotyped using Illumina PorcineSNP60 k. The strongest associations with backfat contents of palmitic, palmitoleic, oleic, medium-chain and long-chain FAs were found for the Sus scrofa chromosome (SSC) 8 region located at 119 to 122 Mb, where the gene ELOVL FA elongase 6 is mapped. Palmitic, palmitoleic, stearic and oleic acid contents were also found associated with SSC14, in particular with the genomic region at 121 to 124 Mb, where stearoyl-CoA desaturase Δ9 gene lies. On the other hand, the genomic regions associated with backfat contents of arachidic, arachidonic, n-6 and n-3 FAs showed to harbour mainly genes involved in dietary lipids and carbohydrates digestion, absorption and utilisation. To our knowledge, this is the first study performed in Large White pigs identifying markers and genomic regions associated with backfat FA composition. The results validate in Large White some associations previously detected in other pig breeds and indicate the involvement of distinct metabolic pathways in the deposition pattern of essential and non-essential FAs.
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20
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Viterbo VS, Lopez BIM, Kang H, Kim H, Song CW, Seo KS. Genome wide association study of fatty acid composition in Duroc swine. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018. [PMID: 29514447 PMCID: PMC6043425 DOI: 10.5713/ajas.17.0779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Objective Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following genome-wide rapid association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively. Genome wide significant variants were located on the same region of swine chromosome 14 (SSC14) that spanned from 120 to 124 Mb. Top SNP ALGA008191 was located at 5 kb near the stearoyl-CoA desaturase (SCD) gene. This gene is directly involved in desaturation of stearic acid into oleic acid. General relationship of significant SNPs showed high linkage disequilibrium thus genome-wide signals was attributed to SCD gene. However, understanding the role of other genes like elongation of very long chain fatty acids-3 (ELOVL3) located on this chromosomal segment might help in further understanding of metabolism and biosynthesis of fatty acids. Conclusion Overall, this study provides evidence that validates SCD gene as strong candidate gene associated with fatty acid composition in Duroc pigs. Moreover, this study confirms significant SNPs near ELOVL3 gene.
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Affiliation(s)
- Vanessa S Viterbo
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea.,Department of Animal Science, College of Agriculture, Central Luzon State University, Science City of Muńoz, 3120, Philippines
| | - Bryan Irvine M Lopez
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Hyunsung Kang
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Hoonseop Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Choul-Won Song
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
| | - Kang Seok Seo
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea
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21
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Revilla M, Puig-Oliveras A, Crespo-Piazuelo D, Criado-Mesas L, Castelló A, Fernández AI, Ballester M, Folch JM. Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions. Sci Rep 2018; 8:2045. [PMID: 29391556 PMCID: PMC5794915 DOI: 10.1038/s41598-018-20473-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19 chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory effects. Remarkably, a SNP in the ACSM5 promoter region and a SNP in the 3′UTR region of FABP4 were the most associated polymorphisms with the ACSM5 and FABP4 expression levels, respectively. Moreover, relevant lipid-related genes mapped in the trans-eQTLs regions associated with the ACSM5, FABP4, FADS2, and SLC27A4 genes. Interestingly, a trans-eQTL hotspot on SSC13 regulating the gene expression of ELOVL6, ELOLV5, and SCD, three important genes implicated in the elongation and desaturation of fatty acids, was identified. These findings provide new data to further understand the functional regulatory mechanisms implicated in the variation of fatty acid composition in pigs.
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Affiliation(s)
- Manuel Revilla
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
| | - Anna Puig-Oliveras
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Daniel Crespo-Piazuelo
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Lourdes Criado-Mesas
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Anna Castelló
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Josep M Folch
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
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22
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Liu H, Liu J, Zhou T, Wang G, Lu K, Zhang T, Li L, Wang J. The contributions of hepatic de novo lipogenesis to the difference in body fat mass of genetically lean and fat duck breeds. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1411264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Junying Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Tianyu Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Guosong Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Kai Lu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Tao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People’s Republic of China
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23
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Zhang J, Cui L, Ma J, Chen C, Yang B, Huang L. Transcriptome analyses reveal genes and pathways associated with fatty acid composition traits in pigs. Anim Genet 2017; 48:645-652. [DOI: 10.1111/age.12597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 11/30/2022]
Affiliation(s)
- J. Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
| | - L. Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
| | - J. Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
| | - C. Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
| | - B. Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
| | - L. Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; 330045 Nanchang China
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24
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van Son M, Enger EG, Grove H, Ros-Freixedes R, Kent MP, Lien S, Grindflek E. Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs. BMC Genomics 2017; 18:369. [PMID: 28494783 PMCID: PMC5426056 DOI: 10.1186/s12864-017-3752-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace. Results Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7. Conclusions This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3752-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maren van Son
- Norsvin SA, Storhamargata 44, , 2317, Hamar, Norway.
| | | | - Harald Grove
- Centre for Integrative Genetics (CIGENE), Department for Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P. O. Box 5003, 1432, Ås, Norway
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 191 Av Alcalde Rovira Roure, 25198, Lleida, Catalonia, Spain.,Present address: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, EH25 9RG, Midlothian, Scotland, UK
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department for Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P. O. Box 5003, 1432, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department for Animal and Aquacultural Sciences, Norwegian University of Life Sciences, P. O. Box 5003, 1432, Ås, Norway
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25
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Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Suzuki K. Genome-wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population. Anim Sci J 2017; 88:1482-1490. [PMID: 28402008 DOI: 10.1111/asj.12793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/15/2017] [Indexed: 12/24/2022]
Abstract
The aim of the present study was to detect quantitative trait loci affecting fatty acid composition in back fat and intramuscular fat in a Duroc pig population comprising seventh-generation pedigrees using genome-wide association studies (GWAS). In total, 305 animals were genotyped using single nucleotide polymorphisms (SNPs) array and five selected SNPs from regions containing known candidate genes related to fatty acid synthesis or metabolism. In total, 24 genome-wide significant SNP regions were detected in 12 traits, and 76 genome-wide suggestive SNP regions were detected in 33 traits. The Sus scrofa chromosome (SSC) 7 at 10.3 Mb was significantly associated with C17:0 in intramuscular fat, while the SSC9 at 13.6 Mb was significantly associated with C14:0 in intramuscular fat. The SSC12 at 1.0 Mb was significantly associated with C14:0 in back fat and the SSC14 at 121.0 Mb was significantly associated with C18:0 in intramuscular fat. These regions not only replicated previously reported loci containing some candidate genes involved in fatty acid composition (fatty acid synthase and stearoyl-CoA desaturase) but also included several additional related loci.
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Affiliation(s)
- Shuji Sato
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | | | - Takashi Kikuchi
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Sachiko Egawa
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, Japan
| | - Kimiko Kohira
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Tomomi Saito
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Hironori Sakuma
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Satoshi Miyashita
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, Japan
| | - Shinji Arata
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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26
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Zheng X, Kuang Y, Lv W, Cao D, Sun Z, Sun X. Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio). PLoS One 2016; 11:e0169127. [PMID: 28030623 PMCID: PMC5193488 DOI: 10.1371/journal.pone.0169127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/12/2016] [Indexed: 12/24/2022] Open
Abstract
Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.
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Affiliation(s)
- Xianhu Zheng
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Youyi Kuang
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Weihua Lv
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Dingchen Cao
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Zhipeng Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Xiaowen Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- * E-mail:
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27
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Supakankul P, Kumchoo T, Mekchay S. Identification and characterization of novel single nucleotide polymorphism markers for fat deposition in muscle tissue of pigs using amplified fragment length polymorphism. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:338-346. [PMID: 27608636 PMCID: PMC5337912 DOI: 10.5713/ajas.16.0200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/26/2016] [Accepted: 09/08/2016] [Indexed: 02/07/2023]
Abstract
Objective This study was conducted to identify and evaluate the effective single nucleotide polymorphism (SNP) markers for fat deposition in the longissimus dorsi muscles of pigs using the amplified fragment length polymorphism (AFLP) approach. Methods Sixty-four selective primer combinations were used to identify the AFLP markers in the 20 highest- and 20 lowest-intramuscular fat (IMF) content phenotypes. Five AFLP fragments were converted into simple codominant SNP markers. These SNP markers were tested in terms of their association with IMF content and fatty acid (FA) composition traits in 620 commercially crossbred pigs. Results The SSC7 g.4937240C>G marker showed an association with IMF content (p<0.05). The SSC9 g.5496647_5496662insdel marker showed a significant association with IMF content and arachidonic levels (p<0.05). The SSC10 g.71225134G>A marker revealed an association with palmitoleic and ω9 FA levels (p<0.05), while the SSC17 g.61976696G>T marker showed a significant association with IMF content and FA levels of palmitoleic, eicosenoic, arachidonic, monounsaturated fatty acids, and ω9 FA levels. However, no significant association of SSC8 g.47338181G>A was observed with any IMF and FA levels in this study. Conclusion Four SNP markers (SSC7 g.4937240C>G, SSC9 g.5496647_5496662insdel, SSC10 g.71225134G>A, and SSC17 g.61976696G>T) were found to be associated with IMF and/or FA content traits in commercially crossbred pigs. These findings provide evidence of the novel SNP markers as being potentially useful for selecting pigs with the desirable IMF content and FA composition.
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Affiliation(s)
- Pantaporn Supakankul
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.,Human and Animal Biotechnology Program, Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Tanavadee Kumchoo
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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28
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Zhang W, Bin Yang, Zhang J, Cui L, Ma J, Chen C, Ai H, Xiao S, Ren J, Huang L. Genome-wide association studies for fatty acid metabolic traits in five divergent pig populations. Sci Rep 2016; 6:24718. [PMID: 27097669 PMCID: PMC4838829 DOI: 10.1038/srep24718] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/05/2016] [Indexed: 01/09/2023] Open
Abstract
Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition.
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Affiliation(s)
- Wanchang Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Junjie Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Leilei Cui
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Junwu Ma
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
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Ros-Freixedes R, Gol S, Pena RN, Tor M, Ibáñez-Escriche N, Dekkers JCM, Estany J. Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs. PLoS One 2016; 11:e0152496. [PMID: 27023885 PMCID: PMC4811567 DOI: 10.1371/journal.pone.0152496] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/15/2016] [Indexed: 11/23/2022] Open
Abstract
Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.
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Affiliation(s)
- Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- * E-mail: (RRF); (JE)
| | - Sofia Gol
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Ramona N. Pena
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Marc Tor
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Noelia Ibáñez-Escriche
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- IRTA, Genètica i Millora Animal, Lleida, Catalonia, Spain
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- * E-mail: (RRF); (JE)
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Stachowiak M, Szczerbal I, Switonski M. Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 140:233-70. [PMID: 27288831 DOI: 10.1016/bs.pmbts.2016.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity.
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Affiliation(s)
- M Stachowiak
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - I Szczerbal
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
| | - M Switonski
- Department of Genetics, Animal Breeding, Poznań University of Life Sciences, Poznań, Poland.
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A genome-wide association analysis for susceptibility of pigs to enterotoxigenic Escherichia coli F41. Animal 2016; 10:1602-8. [PMID: 26936422 DOI: 10.1017/s1751731116000306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a type of pathogenic bacteria that cause diarrhea in piglets through colonizing pig small intestine epithelial cells by their surface fimbriae. Different fimbriae type of ETEC including F4, F18, K99 and F41 have been isolated from diarrheal pigs. In this study, we performed a genome-wide association study to map the loci associated with the susceptibility of pigs to ETEC F41 using 39454 single nucleotide polymorphisms (SNPs) in 667 F2 pigs from a White Duroc×Erhualian F2 cross. The most significant SNP (ALGA0022658, P=5.59×10-13) located at 6.95 Mb on chromosome 4. ALGA0022658 was in high linkage disequilibrium (r 2>0.5) with surrounding SNPs that span a 1.21 Mb interval. Within this 1.21 Mb region, we investigated ZFAT as a positional candidate gene. We re-sequenced cDNA of ZFAT in four pigs with different susceptibility phenotypes, and identified seven coding variants. We genotyped these seven variants in 287 unrelated pigs from 15 diverse breeds that were measured with ETEC F41 susceptibility phenotype. Five variants showed nominal significant association (P<0.05) with ETEC F41 susceptibility phenotype in International commercial pigs. This study provided refined region associated with susceptibility of pigs to ETEC F41 than that reported previously. Further works are needed to uncover the underlying causal mutation(s).
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Guo YM, Zhang ZY, Ma JW, Ai HS, Ren J, Huang LS. A genomewide association study of feed efficiency and feeding behaviors at two fattening stages in a White Duroc × Erhualian F population. J Anim Sci 2016; 93:1481-9. [PMID: 26020169 DOI: 10.2527/jas.2014-8655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Feeding efficiency is a multifactorial and economically important trait in pigs. Genetic improvement of feeding efficiency will greatly benefit the pig industry. In the past decades, the hog market weight has increased worldwide. However, whether the genetic architecture of feeding efficiency is same or not at early and late fattening periods is unclear. To map genomic regions for feed efficiency and feeding behavior traits at early (n ≥ 384) and late (n ≥ 334) growth stages in pigs, we performed genomewide association studies for feed to gain ratio (FCR), residual feed intake (RFI), daily feed intake, daily visit times, daily feeding time (DFT), feed intake per second (FIPS), and feed intake per visit during 3 periods (2 stages and overall) in a White Duroc × Erhualian F2 intercross population. Six chromosomal regions showed significant association with these traits, of which 4 loci were reported for the first time. Our results confirmed the QTL of FCR around 34 Mb on SSC7 and RFI around 134 Mb on SSC12. Of note, 2 regions were associated with more than 1 trait. One was around 36 Mb on SSC7, and there were 47 and 67 SNP associated with FCR from 120 to 210 and from 120 to 240 d, respectively. The top SNP is located in a 2.88-Mb linkage disequilibrium (LD) block that harbors 44 genes. We propose the high mobility group AT-hook 1 gene as a plausible candidate gene in this region. The other was evidenced around 53 Mb on SSC12, which had multiple association signals for DFT and FIPS. The top SNP is located in a 211-kb LD block that harbors only 1 annotated gene, WSCD1, which encodes a protein with sulfotransferase activity and involves the glucose metabolism and, therefore, appears to be a plausible candidate gene. Except the region on SSC12 associated with DFT at both stages, the rest of the regions associated with the traits at only 1 stage, so the genetic architectures of the 2 stages are not same.
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Zhang W, Zhang J, Cui L, Ma J, Chen C, Ai H, Xie X, Li L, Xiao S, Huang L, Ren J, Yang B. Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genet Sel Evol 2016; 48:5. [PMID: 26796620 PMCID: PMC4722735 DOI: 10.1186/s12711-016-0184-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
Background Fatty acid composition in muscle is an important factor that affects the nutritive value and taste of pork. To investigate the genetic architecture of fatty acid composition of pork, we measured fatty acid contents in longissimus dorsi muscle of 1244 pigs from three divergent populations and conducted genome-wide association studies (GWAS) for fatty acid contents. Results We detected 26 genome-wide significant quantitative trait loci (QTL) on eight chromosomes (SSC for Sus scrofa) for eight fatty acids. These loci not only replicated previously reported QTL for C18:0 on SSC14 and C20:0 on SSC16, but also included several novel QTL such as those for C20:1 on SSC7, C14:0 on SSC9, and C14:0, C16:0 and C16:1 on SSC12. Furthermore, we performed a meta-analysis of GWAS on five populations, including the three populations that were investigated in this study and two additional populations that we had previously examined. This enhanced the strength of the associations detected between fatty acid composition and several marker loci, especially for those for C18:0 on SSC14 and C20:0 on SSC16. The genes ELOVL5, ELOVL6, ELOVL7, FASN, SCD and THRSP, which have functions that are directly relevant to fatty acid metabolism, are proximal to the top associated markers at six significant QTL. Conclusions The findings improve our understanding of the genetic architecture of fatty acid composition in pork and contribute to further fine-map and characterize genes that influence fatty acid composition. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0184-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wanchang Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junjie Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Leilei Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Congying Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xianhua Xie
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lin Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Yang J, Huang L, Yang M, Fan Y, Li L, Fang S, Deng W, Cui L, Zhang Z, Ai H, Wu Z, Gao J, Ren J. Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs. Sci Rep 2016; 6:19240. [PMID: 26781738 PMCID: PMC4726066 DOI: 10.1038/srep19240] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/12/2015] [Indexed: 11/25/2022] Open
Abstract
Vertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds.
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Affiliation(s)
- Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.,State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Yin Fan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lin Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Shaoming Fang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Wenjiang Deng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Leilei Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Zhen Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Jun Gao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
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Guo Y, Hou L, Zhang X, Huang M, Mao H, Chen H, Ma J, Chen C, Ai H, Ren J, Huang L. A meta analysis of genome-wide association studies for limb bone lengths in four pig populations. BMC Genet 2015. [PMID: 26219668 PMCID: PMC4518597 DOI: 10.1186/s12863-015-0257-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations. Results We measured the lengths of five limb bones including scapula, humerus, ulna, femur and tibia that were dissected from the right-side carcass of 925, 331, 314 and 434 animals from White Duroc × Erhualian F2 intercross, Erhualian, Laiwu and Sutai populations, respectively. We genotyped the 2004 pigs for 62,163 single nucleotide polymorphisms (SNPs) on the Porcine SNP60 BeadChip, and performed GWAS and a GWAS meta analysis in the 4 populations. In total, we identified 12 and 4 loci associated with the limb bone lengths at suggestive and genome-wide significant levels respectively, of which 4 loci were reported for the first time. The most prominent locus was identified in a 924-kb (kilo base pairs) linkage disequilibrium block on Sus Scrofa chromosome (SSC) 7, and High Mobility Group AT-hook 1 (HMGA1) appears to be a strong candidate gene in this region. Another promising locus is located in the middle of SSC4, and Pleiomorphic Adenoma Gene 1 (PLAG1) is a functionally plausible candidate gene underlying the locus. Because the lengths of the 5 limb bones are highly correlated to each other, most of significant loci were associated with all of the 5 traits; however, several loci showed specific effect on the length of one limb bone, such as the locus at the proximal end of SSC2 associated with only the scapula length. Conclusion To our knowledge, this study was the first GWAS meta analysis for limb bone lengths in pigs. As expected, the meta analysis is more powerful to identify genomic loci. A total of 16 loci were identified in this study, including four novel loci. HMGA1 and PLAG1 are two appearing candidate genes for pig limb bone lengths, which warrant further investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0257-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanmei Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lijuan Hou
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xufei Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. .,Current address: Wenzhou Medical University, WenZhou, 325000, China.
| | - Min Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huirong Mao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hao Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Congying Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Liu X, Xiong X, Yang J, Zhou L, Yang B, Ai H, Ma H, Xie X, Huang Y, Fang S, Xiao S, Ren J, Ma J, Huang L. Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population. Genet Sel Evol 2015; 47:44. [PMID: 25962760 PMCID: PMC4427942 DOI: 10.1186/s12711-015-0120-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population. METHODS Three hundred and thirty six Chinese Erhualian and 610 DLY pigs were genotyped using the Illumina PorcineSNP60K Beadchip and evaluated for 20 meat quality traits. After quality control, 35 985 and 56 216 single nucleotide polymorphisms (SNPs) were available for the Chinese Erhualian and DLY datasets, respectively, and were used to perform two separate GWAS. We also performed a meta-analysis that combined P-values and effects of 29 516 SNPs that were common to Erhualian, DLY, F2 and Sutai pig populations. RESULTS We detected 28 and nine suggestive SNPs that surpassed the significance level for meat quality in Erhualian and DLY pigs, respectively. Among these SNPs, ss131261254 on pig chromosome 4 (SSC4) was the most significant (P = 7.97E-09) and was associated with drip loss in Erhualian pigs. Our results suggested that at least two QTL on SSC12 and on SSC15 may have pleiotropic effects on several related traits. All the QTL that were detected by GWAS were population-specific, including 12 novel regions. However, the meta-analysis revealed seven novel QTL for meat characteristics, which suggests the existence of common underlying variants that may differ in frequency across populations. These QTL regions contain several relevant candidate genes. CONCLUSIONS These findings provide valuable insights into the molecular basis of convergent evolution of meat quality traits in Chinese and Western breeds that show divergent phenotypes. They may contribute to genetic improvement of purebreds for crossbred performance.
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Affiliation(s)
- Xianxian Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xinwei Xiong
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jie Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lisheng Zhou
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huanban Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Yixuan Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shaoming Fang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China.
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Qiao R, Gao J, Zhang Z, Li L, Xie X, Fan Y, Cui L, Ma J, Ai H, Ren J, Huang L. Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations. Genet Sel Evol 2015; 47:17. [PMID: 25885760 PMCID: PMC4358731 DOI: 10.1186/s12711-015-0089-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population. RESULTS We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits. CONCLUSIONS We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.
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Affiliation(s)
- Ruimin Qiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Jun Gao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Lin Li
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Yin Fan
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Leilei Cui
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
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Cui L, Zhang J, Ma J, Guo Y, Li L, Xiao S, Ren J, Yang B, Huang L. Sexually dimorphic genetic architecture of complex traits in a large-scale F2 cross in pigs. Genet Sel Evol 2014; 46:76. [PMID: 25374066 PMCID: PMC4221709 DOI: 10.1186/s12711-014-0076-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND It is common for humans and model organisms to exhibit sexual dimorphism in a variety of complex traits. However, this phenomenon has rarely been explored in pigs. RESULTS To investigate the genetic contribution to sexual dimorphism in complex traits in pigs, we conducted a sex-stratified analysis on 213 traits measured in 921 individuals produced by a White Duroc × Erhualian F2 cross. Of the 213 traits examined, 102 differed significantly between the two sexes (q value <0.05), which indicates that sex is an important factor that influences a broad range of traits in pigs. We compared the estimated heritability of these 213 traits between males and females. In particular, we found that traits related to meat quality and fatty acid composition were significantly different between the two sexes, which shows that genetic factors contribute to variation in sexual dimorphic traits. Next, we performed a genome-wide association study (GWAS) in males and females separately; this approach allowed us to identify 13.6% more significant trait-SNP (single nucleotide polymorphism) associations compared to the number of associations identified in a GWAS that included both males and females. By comparing the allelic effects of SNPs in the two sexes, we identified 43 significant sexually dimorphic SNPs that were associated with 22 traits; 41 of these 43 loci were autosomal. The most significant sexually dimorphic loci were found to be associated with muscle hue angle and Minolta a* values (which are parameters that reflect the redness of meat) and were located between 9.3 and 10.7 Mb on chromosome 6. A nearby gene i.e. NUDT7 that plays an important role in heme synthesis is a strong candidate gene. CONCLUSIONS This study illustrates that sex is an important factor that influences phenotypic values and modifies the effects of the genetic variants that underlie complex traits in pigs; it also emphasizes the importance of stratifying by sex when performing GWAS.
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Affiliation(s)
- Leilei Cui
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Junjie Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Yuanmei Guo
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Lin Li
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
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