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Przybylska P, Kuczaj M. Relationship between Selected SNPs (g.16024A/G, g.16039T/C and g.16060A/C) of the FASN Gene and the Fat Content and Fatty Acid Profile in the Milk of Three Breeds of Cows. Animals (Basel) 2024; 14:1934. [PMID: 38998046 PMCID: PMC11240365 DOI: 10.3390/ani14131934] [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: 05/20/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
Fat is an important energy and nutritional component of milk and consists of fatty acids. FASN (fatty acid synthase) is an enzyme that regulates the synthesis of fatty acids in the milk and meat of cattle. It was hypothesized that knowing the relationships between the genotypes of the tested single nucleotide polymorphisms (SNPs) and the content of fat and specific fatty acids would make it possible to improve milk quality in the selection process during cattle breeding. This study aimed to analyze the relationships of SNPs (g.16024A/G, g.16039T/C) of the FASN gene and their genotypes with the fat and fatty acid content of the milk of the following breeds: Polish Red-White (ZR), Polish Red (RP), and Polish Holstein-Friesian Red-White (RW). The SNP g.16060A/C was included in the study, although its effect on the fat composition of cow's milk has not yet been widely studied. Milk was obtained during test milkings. SNP genotyping was performed using the real-time PCR (HRM) method. The milk from ZR and RP cows was more often characterized by a more favorable fatty acid profile than the milk from RW cows. This information can be used by cattle breeders and consumers of so-called functional food.
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Affiliation(s)
- Paulina Przybylska
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, ul. Chelmonskiego 38C, 50-375 Wroclaw, Poland
| | - Marian Kuczaj
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, ul. Chelmonskiego 38C, 50-375 Wroclaw, Poland
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Liu SS, Bai TT, Que TL, Luo A, Liang YX, Song YX, Liu TY, Chen JW, Li J, Li N, Zhang ZC, Chen NN, Liu Y, Zhang ZC, Zhou YL, Wang X, Zhu ZB. PI3K/AKT mediated De novo fatty acid synthesis regulates RIG-1/MDA-5-dependent type I IFN responses in BVDV-infected CD8 +T cells. Vet Microbiol 2024; 291:110034. [PMID: 38432076 DOI: 10.1016/j.vetmic.2024.110034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Bovine viral diarrhea virus (BVDV) has caused massive economic losses in the cattle business worldwide. Fatty acid synthase (FASN), a key enzyme of the fatty acid synthesis (FAS) pathway, has been shown to support virus replication. To investigate the role of fatty acids (FAs) in BVDV infection, we infected CD8+T lymphocytes obtained from healthy cattle with BVDV in vitro. During early cytopathic (CP) and noncytopathic (NCP) BVDV infection in CD8+ T cells, there is an increase in de novo lipid biosynthesis, resulting in elevated levels of free fatty acids (FFAs) and triglycerides (TG). BVDV infection promotes de novo lipid biosynthesis in a dose-dependent manner. Treatment with the FASN inhibitor C75 significantly reduces the phosphorylation of PI3K and AKT in BVDV-infected CD8+ T cells, while inhibition of PI3K with LY294002 decreases FASN expression. Both CP and NCP BVDV strains promote de novo fatty acid synthesis by activating the PI3K/AKT pathway. Further investigation shows that pharmacological inhibitors targeting FASN and PI3K concurrently reduce FFAs, TG levels, and ATP production, effectively inhibiting BVDV replication. Conversely, the in vitro supplementation of oleic acid (OA) to replace fatty acids successfully restored BVDV replication, underscoring the impact of abnormal de novo fatty acid metabolism on BVDV replication. Intriguingly, during BVDV infection of CD8+T cells, the use of FASN inhibitors prompted the production of IFN-α and IFN-β, as well as the expression of interferon-stimulated genes (ISGs). Moreover, FASN inhibitors induce TBK-1 phosphorylation through the activation of RIG-1 and MDA-5, subsequently activating IRF-3 and ultimately enhancing the IFN-1 response. In conclusion, our study demonstrates that BVDV infection activates the PI3K/AKT pathway to boost de novo fatty acid synthesis, and inhibition of FASN suppresses BVDV replication by activating the RIG-1/MDA-5-dependent IFN response.
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Affiliation(s)
- Shan-Shan Liu
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Tong-Tong Bai
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Tao-Lin Que
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - An Luo
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Yu-Xin Liang
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Yu-Xin Song
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Tian-Yi Liu
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Jin-Wei Chen
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Jing Li
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Nan Li
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Ze-Chen Zhang
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Nan-Nan Chen
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Yu Liu
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Ze-Cai Zhang
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Yu-Long Zhou
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Xue Wang
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China
| | - Zhan-Bo Zhu
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs, Daqing 163319, China; Engineering Research Center for Prevention and Control of Cattle Diseases, Heilongjiang Province, Daqing 163319, China.
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Ardicli S, Dincel D, Samli H, Senturk N, Karalar B, Unlu S, Soyudal B, Kubad E, Balci F. Association of polymorphisms in lipid and energy metabolism-related genes with fattening performance in Simmental cattle. Anim Biotechnol 2023; 34:3428-3440. [PMID: 36459440 DOI: 10.1080/10495398.2022.2152557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Lipid and energy metabolism are major constituents of mammal growth and thus fattening performance of cattle. This study was designed to evaluate the effects of polymorphisms in lipid and energy metabolism-related genes including oxidized low-density lipoprotein receptor 1 (OLR1), lactoferrin (LTF), stearoyl-CoA desaturase (SCD), beta-lactoglobulin (LGB), thyroglobulin (TG), annexin A9 (ANXA9), myogenic factor 5 (MYF5), protein kinase AMP-activated non-catalytic subunit gamma 3 (PRKAG3), and pituitary-specific transcriptional factor 1 (PIT1), on fattening performance in Simmental cattle. A total of 72 purebred Simmental bulls with a similar initial age and weight were fattened on the same farm for 10 months. Association analysis was performed using linear mixed models. The OLR1 marker was significantly associated with the final weight (FW), hot carcass weight (HCW), chilled carcass weight (CCW), dressing percentage (DP), and total weight gain (TWG). SCD affected the FW, TWG, and average daily live weight gain (ADWG). The present results clearly demonstrated the significant impact of the TG marker on fattening performance. It was highly significantly associated with the FW, HCW, CCW, and TWG. The SCD × TG and the OLR1 × TG interactions had remarkable effects on the traits analyzed. The GACC and CCCC haplotypes of the SCD × TG and OLR1 × TG, respectively, were found to be powerful markers for fattening performance in Simmentals. Novel associations in this study may be useful for further genetic evaluations to improve beef cattle breeding.
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Affiliation(s)
- Sena Ardicli
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Deniz Dincel
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Hale Samli
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Nursen Senturk
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Beyza Karalar
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Bursa Uludag University, Bursa, Turkey
| | - Sıla Unlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey
| | | | - Evrim Kubad
- Department of Animal Nutrition and Nutritional Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Faruk Balci
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
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Sycheva I, Latynina E, Mamedov A, Tsibizova O, Kozak Y, Svistounov D, Bystrenina I, Orishev A. Effect of TG5 and LEP polymorphisms on the productivity, chemical composition, and fatty acid profile of meat from Simmental bulls. Vet World 2023; 16:1647-1654. [PMID: 37766707 PMCID: PMC10521186 DOI: 10.14202/vetworld.2023.1647-1654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/13/2023] [Indexed: 09/29/2023] Open
Abstract
Background and Aim Enhancing the nutritional and biological value of meat obtained from young surplus replacement animals of dual-purpose breeds is a critical objective in the livestock industry. This study aimed to investigate the impact of thyroglobulin (TG5, c. -422C > T) and leptin (LEP, c. 239C > T) polymorphisms on the productivity, chemical composition, and fatty acid (FA) profile of meat from Simmental bulls. Materials and Methods A total of 26 Simmental bulls were genotyped for TG5 (c. -422C > T) and LEP (c. 239C > T) polymorphisms and reared under the same fattening conditions. Controlled slaughter was conducted at 18 months of age. Subsequently, the experimental animals were evaluated to determine their slaughter traits and the chemical and FA composition of ground beef and the longissimus dorsi muscle. Results The results showed that the TG5 (c. -422C > T) polymorphism significantly (p < 0.05) affected the differentiation of bulls in terms of the synthesis of stearic acid, linolenic acid, and total polyunsaturated FAs, as well as the fat and dry matter content in the longissimus dorsi muscle. Conversely, the presence of the T allele in the LEP (c. 239C > T) polymorphism was associated with increased dry matter and fat in ground beef, carcass weight, and internal fat weight. Conclusion The analysis of slaughter traits and the chemical and FA composition of meat from the Simmental bulls genotyped for the TG5 and LEP genes revealed a genetic basis for the quantitative and qualitative characteristics of meat productivity. Thus, the genetic variability of bulls regarding the LEP and TG5 genes can be used to improve the quantitative and qualitative indicators of meat productivity in Simmental cattle through marker-assisted selection.
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Affiliation(s)
- Irina Sycheva
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Evgeniya Latynina
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Azer Mamedov
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Oksana Tsibizova
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Yulia Kozak
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Dmitriy Svistounov
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Irina Bystrenina
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
| | - Aleksandr Orishev
- Department of Animal Science and Biology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russian Federation
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Nishio M, Inoue K, Arakawa A, Ichinoseki K, Kobayashi E, Okamura T, Fukuzawa Y, Ogawa S, Taniguchi M, Oe M, Takeda M, Kamata T, Konno M, Takagi M, Sekiya M, Matsuzawa T, Inoue Y, Watanabe A, Kobayashi H, Shibata E, Ohtani A, Yazaki R, Nakashima R, Ishii K. Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle. Anim Sci J 2023; 94:e13883. [PMID: 37909231 DOI: 10.1111/asj.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 11/02/2023]
Abstract
We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.
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Affiliation(s)
- Motohide Nishio
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | - Keiichi Inoue
- National Livestock Breeding Center, Fukushima, Japan
- University of Miyazaki, Miyazaki, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Yo Fukuzawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | - Shinichiro Ogawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Mika Oe
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | | | - Takehiro Kamata
- Aomori Prefectural Industrial Technology Research Center, Tsugaru, Japan
| | - Masaru Konno
- Iwate Agricultural Research Center Animal Industry Research Institute, Takizawa, Japan
| | - Michihiro Takagi
- Miyagi Prefecture Animal Industry Experiment Station, Osaki, Japan
| | - Mario Sekiya
- Akita Prefectural Livestock Experiment Station, Daisen, Japan
| | - Tamotsu Matsuzawa
- Livestock Research Centre, Fukushima Agricultural Technology Centre, Fukushima, Japan
| | - Yoshinobu Inoue
- Tottori Prefectural Livestock Research Center, Tottori, Japan
| | | | - Hiroshi Kobayashi
- Institute of Animal Production Okayama Prefectural Technology Center for Agriculture, Forestry and Fisheries, Misaki, Japan
| | - Eri Shibata
- Hiroshima Prefectural Technology Research Institute, Livestock Technology Research Center, Shobara, Japan
| | - Akihumi Ohtani
- Yamaguchi Prefectural Agriculture and Forestry General Technology Center, Mine, Japan
| | - Ryu Yazaki
- Oita Prefectural Agriculture, Forestry, and Fisheries Research Center, Takeda, Japan
| | - Ryotaro Nakashima
- Cattle Breeding Development Institute of Kagoshima Prefecture, Soo, Japan
| | - Kazuo Ishii
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
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Skeletal muscle gene expression and meat quality of F1 Angus-Nellore young steers and bulls feedlot finished. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Otto JR, Mwangi FW, Pewan SB, Adegboye OA, Malau-Aduli AEO. Lipogenic Gene Single Nucleotide Polymorphic DNA Markers Associated with Intramuscular Fat, Fat Melting Point, and Health-Beneficial Omega-3 Long-Chain Polyunsaturated Fatty Acids in Australian Pasture-Based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu Beef Cattle. Genes (Basel) 2022; 13:genes13081411. [PMID: 36011322 PMCID: PMC9407580 DOI: 10.3390/genes13081411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
This study used targeted sequencing aimed at identifying single nucleotide polymorphisms (SNP) in lipogenic genes and their associations with health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP) of the M. longissimus dorsi muscle in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu cattle. It was hypothesized that SNP encoding for the fatty acid-binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and fatty acid synthase (FASN) genes will be significantly associated with health-beneficial n-3 LC-PUFA and the meat eating quality traits of IMF and FMP in an Australian pasture-based beef production system. Two SNP mutations, g.21267406 T>C and g.21271264 C>A, in the SCD gene were significantly (p < 0.05) associated with IMF, FMP, oleic acid (18:1n-9), linoleic acid (LA) 18:2n-6, alpha-linolenic acid (ALA) 18:3n-3, eicosapentaenoic acid (EPA) 20:5n-3, docosahexaenoic acid (DHA) 22:6-n-3, and docosapentaenoic acid (DPA) 22:5n-3. Significant positive correlations (p < 0.05) between FASN SNP g. 50787138 A>G and FMP, 18:1n-9, ALA, EPA, DHA, DPA, and total n-3 LC-PUFA were also detected. An SNP (g.44678794 G>A) in the FABP4 gene was associated with FMP. These results provide significant insights into the contributions of lipogenic genes to intramuscular fat deposition and the biosynthesis of health-beneficial n-3 LC-PUFA. The findings also unravel the potential use of lipogenic gene polymorphisms in marker-assisted selection to improve the content of health-promoting n-3 LC-PUFA and meat eating quality traits in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu beef cattle.
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Affiliation(s)
- John R. Otto
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
| | - Felista W. Mwangi
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
| | - Shedrach B. Pewan
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- National Veterinary Research Institute, PMB 01, Vom 930001, Plateau State, Nigeria
| | - Oyelola A. Adegboye
- Public Health and Tropical Medicine Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
| | - Aduli E. O. Malau-Aduli
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Correspondence: ; Tel.: +61-747-815-339
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Stolpovsky YA, Kuznetsov SB, Solodneva EV, Shumov ID. New Cattle Genotyping System Based on DNA Microarray Technology. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Towards Sustainable Sources of Omega-3 Long-Chain Polyunsaturated Fatty Acids in Northern Australian Tropical Crossbred Beef Steers through Single Nucleotide Polymorphisms in Lipogenic Genes for Meat Eating Quality. SUSTAINABILITY 2022. [DOI: 10.3390/su14148409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This study aimed to identify single nucleotide polymorphisms (SNP) in lipogenic genes of northern Australian tropically adapted crossbred beef cattle and to evaluate associations with healthy lipid traits of the Longissimus dorsi (loin eye) muscle. The hypothesis tested was that there are significant associations between SNP loci encoding for the fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD) and fatty acid synthase (FASN) genes and human health beneficial omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA) within the loin eye muscle of northern Australian crossbred beef cattle. Brahman, Charbray, and Droughtmaster crossbred steers were fed on Rhodes grass hay augmented with desmanthus, lucerne, or both, for 140 days and the loin eye muscle sampled for intramuscular fat (IMF), fat melting point (FMP), and fatty acid composition. Polymorphisms in FABP4, SCD, and FASN genes with significant effects on lipid traits were identified with next-generation sequencing. The GG genotype at the FABP4 g.44677239C>G locus was associated with higher proportion of linoleic acid than the CC and CG genotypes (p < 0.05). Multiple comparisons of genotypes at the SCD g.21266629G>T locus indicated that the TT genotype had significantly higher eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids than GG genotype (p < 0.05). Significant correlations (p < 0.05) between FASN SNP and IMF, saturated and monounsaturated fatty acids were observed. These results provide insights into the contribution of lipogenic genes to intramuscular fat deposition and SNP marker-assisted selection for improvement of meat-eating quality, with emphasis on alternate and sustainable sources of ω3 LC-PUFA, in northern Australian tropical crossbred beef cattle, hence an acceptance of the tested hypothesis.
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Al-Thuwaini TM, Aqeel Kareem Z. Dr. Novel missense variant L46Q of fatty acid synthase gene and fatty acids content in Awassi sheep. ACTA SCIENTIARUM: ANIMAL SCIENCES 2022. [DOI: 10.4025/actascianimsci.v44i1.56273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This study was conducted to investigate the association between the polymorphism of the FASN gene with fatty acid content in Awassi sheep. A total of 100 male Awassi sheep between the ages of one and two and a half years old were used in this study. Phenotypic measurement was recorded at slaughter, and from each animal, the longissimus dorsi (LD) muscle samples were taken to analyze the fatty acid profile. Genotyping, sequencing reactions, and in silico tools were performed to confirm the variants in amplified fragments. The result of genotyping revealed two genotypes (AA and AB) of the ovine FASN gene (exon 3). Novel SNP (L46Q) was discovered only within the FASN gene (AB genotype). All utilized in silico tools revealed remarkably deleterious effects for the L46Q on the mutant protein structure, function, and stability. Association analysis revealed that the AB genotype has significantly (p < 0.05) higher levels of animal length and monounsaturated fatty acids (MUFA) with lower amounts of saturated fatty acids (SFA) content than the AA genotype. In conclusion, novel SNP (L46Q) was discovered within the FASN gene (AB genotype), made the animals that has the AB genotype associated with good meat quality traits and this polymorphism may serve as markers for meat quality.
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11
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Association of variants in FABP4, FASN, SCD, SREBP1 and TCAP genes with intramuscular fat, carcass traits and body size in Chinese Qinchuan cattle. Meat Sci 2022; 192:108882. [PMID: 35714427 DOI: 10.1016/j.meatsci.2022.108882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 12/17/2022]
Abstract
This study aimed to genotype the variants in FABP4, FASN, SCD, SREBP1 and TCAP genes, and to analyze their associations with intramuscular fat (IMF) content, carcass traits and body size in Chinese Qinchuan cattle (QC). The association studies showed that the FABP4 c.220A > G polymorphism was significantly associated with ultrasound longissimus muscle depth (ULMD) and IMF, the FASN g.16024A > G polymorphism was significantly associated with ULMD and some body size traits, the SREBP1 84 bp indel was significantly associated with back fat thickness, ULMD and some body size traits. The frequencies of well-characterized A allele in FABP4 c.220A > G in Korean cattle (KOR) and Japanese Black cattle (JB), T allele in SCD g.8586C > T in KOR, SS genotype in SREBP1 84 bp indel in KOR and JB, DELDEL genotype in TCAP g.592-597CTGCAGinsdel in KOR were significantly higher than in Chinese cattle breeds. Thus, the associated four polymorphisms were expected to be genetic selection markers for meat quality, carcass traits and body size of QC.
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Ma X, Wu J, Li Y, Liang X, Casper D, Ding W, Wang X, Shi A, Shi X, Ma L, Eer H, Lang X. Transcriptome and metabolome analyses reveal muscle changes in Tan sheep (Ovis aries) at different ages. Livest Sci 2022. [DOI: 10.1016/j.livsci.2021.104781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle. Animals (Basel) 2021; 11:ani11082424. [PMID: 34438882 PMCID: PMC8388739 DOI: 10.3390/ani11082424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock is an important commodity playing a major role in the global economy. Red meat plays an important role in human life, as it is a good source of animal protein and energy. The fatty acid content of beef has been shown to impact the eating experience and nutritional value of beef. Therefore, this study aimed to identify genomic regions which can account for genetic variation in meat fatty acid content. Genotypes imputed to the Illumina BovineHD 770K BeadChip were used in this study. Thirty-six 1-Mb genomic regions with a posterior probability of inclusion (PPI) greater than 0.90 were identified to be associated with variation in the content of at least one fatty acid. The genomic regions (1Mb) which were associated with more than one fatty acid trait with high genetic variance and harbored good candidate genes were on Chromosome (Chr) 6 (fatty acid binding protein 2), Chr 19 (thyroid hormone receptor alpha, fatty acid synthase), Chr 26 (stearoyl-CoA desaturase), and Chr 29 (thyroid hormone responsive, fatty acid desaturase 2, and fatty acid desaturase 3). Further studies are required to identify the causal variants within the identified genomic regions. Findings from the present study will help to increase understanding of the variation in fatty acid content of beef and help to enhance selection for beef with improved fatty acid composition.
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Gamarra D, Aldai N, Arakawa A, de Pancorbo MM, Taniguchi M. Effect of a genetic polymorphism in SREBP1 on fatty acid composition and related gene expression in subcutaneous fat tissue of beef cattle breeds. Anim Sci J 2021; 92:e13521. [PMID: 33554418 DOI: 10.1111/asj.13521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 12/25/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Sterol regulatory element-binding factor 1 (SREBP1) plays an important role in the lipogenesis which affects fatty acid (FA) composition in backfat and consequently influences beef nutritional quality. This study analyzed the association of 84 bp-indel, both short (S) and long (L) alleles in intron 5 of SREBP1, with FA composition and gene expression of SREBP1 in backfat of northern Spanish beef breeds (Pirenaica, Salers and Holstein-Friesian). Phylogenetic analysis suggests that 84 bp-indel of ruminants is a highly conserved region compared with those in the full-length sequence of intron 5 or mRNA of SREBP1 among species. Overall, higher content of polyunsaturated FAs was observed in SL genotype compared to LL genotype of 84 bp-Indel (p < .05). In particular, in Pirenaica, SL genotype was associated with a higher content of stearic (18:0), α-linolenic (18:3n-3) acid, and total n-3 content (p < .05). However, the gene expression of SREBP1 did not differ among genotypes of 84 bp-Indel (p > .05).
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Affiliation(s)
- David Gamarra
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Noelia Aldai
- Lactiker Research Group, Pharmacy & Food Sciences Department, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Aisaku Arakawa
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Marian M de Pancorbo
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Masaaki Taniguchi
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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Effect of Five Polymorphisms on Percentage of Oleic Acid in Beef and Investigation of Linkage Disequilibrium to Confirm the Locations of Quantitative Trait Loci on BTA19 in Japanese Black Cattle. Life (Basel) 2021; 11:life11070597. [PMID: 34206576 PMCID: PMC8303249 DOI: 10.3390/life11070597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Five polymorphisms associated with the percentage of oleic acid (C18:1) in beef fat were previously reported on bovine chromosome 19 in different Japanese Black cattle populations. This study aimed to verify the effects of these five polymorphisms on C18:1 using the same Japanese Black cattle population and conduct linkage disequilibrium (LD) analysis in order to determine the locations of the quantitative trait loci (QTLs). We genotyped the five polymorphisms (SREBP1 c.1065 + 83 (84bp indel), STARD3 c.1187 C > T, GH c.379 C > G, FASN g.841 G > C, and FASN g.16024 A > G) in two populations, which were bred in Hyogo and Gifu Prefectures, Japan (n = 441 and 443, respectively) in order to analyze their effects on C18:1 using analysis of variance (ANOVA). In the Hyogo population, SREBP1 c.1065 + 83 and STARD3 c.1187 C > T were significantly associated with C18:1 (p < 0.001). Meanwhile, FASN g.841 G > C, FASN g.16024 A > G, and GH c.379 C > G were significantly associated with C18:1 (p < 0.01) in the Gifu population. LD analysis was subsequently conducted to detect the range of the QTLs, which ranged from 32.2 to 46.4 Mbp and from 47.8 to 52.1 Mbp in the Hyogo and Gifu populations, respectively. In conclusion, this study confirmed the existence of QTLs on BTA19 and divided the candidate region for each QTL based on LD coefficients. These results could contribute to efficient searches for responsible genes and polymorphisms for fatty acid composition.
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Wang L, Zhang Y, Zhang B, Zhong H, Lu Y, Zhang H. Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs. BMC Genomics 2021; 22:441. [PMID: 34118873 PMCID: PMC8201413 DOI: 10.1186/s12864-021-07764-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Background Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation. Results A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR). Conclusions This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07764-2.
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Affiliation(s)
- Liyuan Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.,National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Yunfeng Lu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.
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Zalewska M, Puppel K, Sakowski T. Associations between gene polymorphisms and selected meat traits in cattle - A review. Anim Biosci 2021; 34:1425-1438. [PMID: 33561332 PMCID: PMC8495340 DOI: 10.5713/ab.20.0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Kamila Puppel
- Institute of Animal Science, Warsaw University of Life Sciences, Warsaw 02-786, Poland
| | - Tomasz Sakowski
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences (PAS), Magdalenka 05-552, Poland
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Pećina M, Ivanković A. Candidate genes and fatty acids in beef meat, a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1991240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mateja Pećina
- Zavod za specijalno stočarstvo, Sveučilište u Zagrebu Agronomski fakultet, Zagreb, Hrvatska
| | - Ante Ivanković
- Zavod za specijalno stočarstvo, Sveučilište u Zagrebu Agronomski fakultet, Zagreb, Hrvatska
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Belhaj K, Mansouri F, Benmoumen A, Sindic M, Fauconnier ML, Boukharta M, Serghini CH, Elamrani A. Fatty acids, health lipid indices, and cholesterol content of sheep meat of three breeds from Moroccan pastures. Arch Anim Breed 2020; 63:471-482. [PMID: 33473372 PMCID: PMC7810224 DOI: 10.5194/aab-63-471-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/02/2020] [Indexed: 11/21/2022] Open
Abstract
The lipid analysis of commercial lamb's meat, from two main Moroccan production areas Middle Atlas and highlands of eastern Morocco, was conducted. This study concerns the lipid quality of sheep meat from Beni Guil (BG) and Timahdite (Ti) as indigenous breeds and that of the Ouled Djellal (ODj) breed of Algerian origin. To study the effect of the geographical area, the meat samples from the Beni Guil breed were taken in the two main locations of this breed: in the region of Ain Beni Mathar (BGA) and that of Tendrara (BGT). The fatty acid profiles of the sheep meats analyzed showed the following: (i) polyunsaturated fatty acid (PUFA) richness was of 12.87 % and 20.59 % respectively for BGA and BGT breeds; (ii) polyunsaturated / saturated fatty acid ratios were ranged between 0.28 to 0.50 respectively for BGA and Ti breed; and (iii) PUFA- n - 3 content was 1.71 % for ODj breed and 2.13 % for BGA. Thus, the PUFA- n - 6 / PUFA n - 3 ratios range between 4.92 and 9.6 for BGA and Ti sheep meat, respectively. The cholesterol content was 0.08 % and 0.12 % of fresh meat respectively for ODj and BGA. Finally, meats of BGA and ODj have similar thrombogenicity (1.23 and 1.27 respectively) and atherogenicity indices (0.71 and 0.68 respectively). Statistically, these values were significantly higher than those registered for Ti breed (IT: 1.04 and AI: 0.51). In conclusion, from a nutritional point of view, it can be deduced that these meats have an interesting lipid quality due to their richness in desirable fatty acid (UFA + C18 : 0).
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Affiliation(s)
- Kamal Belhaj
- Laboratory for Improving Agricultural Productions, Biotechnology and Environment (LAPABE),
Faculty of Sciences, University Mohammed First, 717, Oujda, 60000, Morocco
- Analysis Quality and Risk Unit, Laboratory of Food Quality and Safety (QSPA), Gembloux
Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Farid Mansouri
- Laboratory for Improving Agricultural Productions, Biotechnology and Environment (LAPABE),
Faculty of Sciences, University Mohammed First, 717, Oujda, 60000, Morocco
| | - Abdessamad Benmoumen
- Laboratory for Improving Agricultural Productions, Biotechnology and Environment (LAPABE),
Faculty of Sciences, University Mohammed First, 717, Oujda, 60000, Morocco
| | - Marianne Sindic
- Analysis Quality and Risk Unit, Laboratory of Food Quality and Safety (QSPA), Gembloux
Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Marie-Laure Fauconnier
- General and Organic Chemistry Unit, Gembloux Agro Bio-Tech, University of Liège,
Gembloux, 5030, Belgium
| | - Mohamed Boukharta
- Institute of Agricultural Industries, High School of Charlemagne, Huy, 4500, Belgium
| | - C. Hana Serghini
- Laboratory for Improving Agricultural Productions, Biotechnology and Environment (LAPABE),
Faculty of Sciences, University Mohammed First, 717, Oujda, 60000, Morocco
| | - Ahmed Elamrani
- Laboratory for Improving Agricultural Productions, Biotechnology and Environment (LAPABE),
Faculty of Sciences, University Mohammed First, 717, Oujda, 60000, Morocco
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Stolpovsky YA, Piskunov AK, Svishcheva GR. Genomic Selection. I: Latest Trends and Possible Ways of Development. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420090148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Kawaguchi F, Tsuchimura M, Oyama K, Matsuhashi T, Maruyama S, Mannen H, Sasazaki S. Effect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and quality. Arch Anim Breed 2020; 63:9-17. [PMID: 32166108 PMCID: PMC7053510 DOI: 10.5194/aab-63-9-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/22/2019] [Indexed: 11/12/2022] Open
Abstract
Carcass traits have been efficiently improved by recent selection using DNA
markers in beef cattle. Additionally, DNA markers might have an effect on other
traits such as fertility traits; therefore attention should also be paid
to such pleiotropic effects. However, the effects of the markers on both
carcass and fertility traits have never been evaluated in the same
population, since they are generally measured in different populations. The
objective in the current study was to discuss effectiveness of DNA markers
developed for carcass traits through investigation of their effects on
carcass and fertility traits in a population. We genotyped six markers SCD
V293A, FASN g.841G>C, PLAG1 g.49066C>G, NCAPG I442M, DGAT1 K232A, and
EDG1 g.1471620G>T in a Japanese Black cattle population (n=515). To
investigate their effects on carcass and fertility traits, we performed
statistical analysis (ANOVA and the Tukey–Kramer honestly significant difference (HSD) test). In the results,
three of six markers, SCD V293A, NCAPG I442M, and EGD1 g.1471620G>T, were
significantly associated with both carcass and fertility traits.
Remarkably, the same allele for each marker had positive effects on both
traits, suggesting that we would be able to simultaneously improve them
using these markers in this population. However, previous studies reported
that the effects of DNA markers could differ among populations. Therefore,
it is necessary to confirm the effect of the marker in each population
before it is used for improvement.
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Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Miyako Tsuchimura
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, 657-2103, Japan
| | - Tamako Matsuhashi
- Institute of Advanced Technology, Kindai University, Kinokawa, 649-6493, Japan.,Gifu Prefectural Livestock Research Institute, Takayama, 506-0101, Japan
| | - Shin Maruyama
- Gifu Prefectural Livestock Research Institute, Takayama, 506-0101, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results. Animals (Basel) 2020; 10:ani10010123. [PMID: 31940936 PMCID: PMC7023423 DOI: 10.3390/ani10010123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study aimed to evaluate mutations within three candidate genes (SCD, ACACA, FASN) for their effects on fattening and slaughter characteristics, as well as meat quality traits, including intramuscular fat (IMF) level in pork. They were selected within differentially expressed genes activated in response to variable backfat content obtained using the RNA sequencing method. The RNA-seq analysis identifies mutations/SNPs located in the mRNA and could be a useful tool for prediction of genetic markers in farm animals. The results showed that selection for FASN A allele in Polish Large White pigs could lead to improved meat quality traits such as water exudation and meat colour. However, analysed polymorphisms showed only slight effects on fat metabolism and IMF content. Abstract In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.
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Mwangi FW, Charmley E, Gardiner CP, Malau-Aduli BS, Kinobe RT, Malau-Aduli AEO. Diet and Genetics Influence Beef Cattle Performance and Meat Quality Characteristics. Foods 2019; 8:E648. [PMID: 31817572 PMCID: PMC6963535 DOI: 10.3390/foods8120648] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
A comprehensive review of the impact of tropical pasture grazing, nutritional supplementation during feedlot finishing and fat metabolism-related genes on beef cattle performance and meat-eating traits is presented. Grazing beef cattle on low quality tropical forages with less than 5.6% crude protein, 10% soluble starches and 55% digestibility experience liveweight loss. However, backgrounding beef cattle on high quality leguminous forages and feedlot finishing on high-energy diets increase meat flavour, tenderness and juiciness due to improved intramuscular fat deposition and enhanced mono- and polyunsaturated fatty acids. This paper also reviews the roles of stearoyl-CoA desaturase, fatty acid binding protein 4 and fatty acid synthase genes and correlations with meat traits. The review argues that backgrounding of beef cattle on Desmanthus, an environmentally well-adapted and vigorous tropical legume that can persistently survive under harsh tropical and subtropical conditions, has the potential to improve animal performance. It also identifies existing knowledge gaps and research opportunities in nutrition-genetics interactions aimed at a greater understanding of grazing nutrition, feedlot finishing performance, and carcass traits of northern Australian tropical beef cattle to enable red meat industry players to work on marbling, juiciness, tenderness and overall meat-eating characteristics.
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Affiliation(s)
- Felista W. Mwangi
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (F.W.M.); (C.P.G.); (R.T.K.)
| | - Edward Charmley
- CSIRO Agriculture and Food, Private Mail Bag Aitkenvale, Australian Tropical Sciences and Innovation Precinct, James Cook University, Townsville, QLD 4811, Australia;
| | - Christopher P. Gardiner
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (F.W.M.); (C.P.G.); (R.T.K.)
| | - Bunmi S. Malau-Aduli
- College of Medicine and Dentistry, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia;
| | - Robert T. Kinobe
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (F.W.M.); (C.P.G.); (R.T.K.)
| | - Aduli E. O. Malau-Aduli
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (F.W.M.); (C.P.G.); (R.T.K.)
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Leal-Gutiérrez JD, Mateescu RG. Genetic basis of improving the palatability of beef cattle: current insights. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1616299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Wang Z, Ma H, Xu L, Zhu B, Liu Y, Bordbar F, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. Animals (Basel) 2019; 9:ani9060296. [PMID: 31151238 PMCID: PMC6617538 DOI: 10.3390/ani9060296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5'-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population.
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Affiliation(s)
- Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National 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.
| | - Haoran Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National 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.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengli Zhang
- National 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
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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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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Kawaguchi F, Kigoshi H, Fukushima M, Iwamoto E, Kobayashi E, Oyama K, Mannen H, Sasazaki S. Whole-genome resequencing to identify candidate genes for the QTL for oleic acid percentage in Japanese Black cattle. Anim Sci J 2019; 90:467-472. [PMID: 30780197 DOI: 10.1111/asj.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/27/2018] [Indexed: 01/25/2023]
Abstract
In our previous study, we detected a QTL for the oleic acid percentage (C18:1) on BTA9 in Japanese Black cattle through a genome-wide association study (GWAS). In this study, we performed whole-genome resequencing on eight animals with higher and lower C18:1 to identify candidate polymorphisms for the QTL. A total of 39,658 polymorphisms were detected in the candidate region, which were narrowed to 1993 polymorphisms within 23 genes based on allele differences between the high and low C18:1 groups. We subsequently selected three candidate genes, that is, CYB5R4, MED23, and VNN1, among the 23 genes based on their function in fatty acid metabolism. In each candidate gene, three SNPs, that is, CYB5R4 c.*349G > T, MED23 c.3700G > A, and VNN1 c.197C > T, were selected as candidate SNPs to verify their effect on C18:1 in a Japanese Black cattle population (n = 889). The statistical analysis showed that these SNPs were significantly associated with C18:1 (p < 0.05), suggesting that they were candidates for the QTL. In conclusion, we successfully narrowed the candidates for the QTL by detecting possible polymorphisms located within the candidate region. It is expected that the responsible polymorphism can be identified by demonstrating their effect on the gene's function.
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Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Hiroto Kigoshi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Moriyuki Fukushima
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery, Asago, Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai, Japan
| | - Eiji Kobayashi
- Division of Animal Breeding and Reproduction Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Zhang H, Guan W. The response of gene expression associated with intramuscular fat deposition in the longissimus dorsi muscle of Simmental × Yellow breed cattle to different energy levels of diets. Anim Sci J 2019; 90:493-503. [PMID: 30706583 DOI: 10.1111/asj.13170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/28/2018] [Accepted: 12/17/2018] [Indexed: 12/29/2022]
Abstract
This study was designed to estimate dietary energy level on intramuscular fat (IMF) deposition in Simmental × Yellow breed cattle. Results showed that ultimate weight and average daily gain in high and medium energy groups were significantly higher than low-energy group, yet feed conversion ratio was significantly lower. IMF content was significantly increased by dietary energy increasing, whereas longissimus muscle shear force significantly decreased. Serum-free fatty acids, triglycerides and glucose significantly increased by dietary energy increasing, whereas growth hormone (GH) significantly decreased. Enzyme activities of lipoprotein lipase (LPL), fatty acid synthase (FAS), and acetyl-CoA carboxylase (ACC) significantly increased by dietary energy increasing, whereas hormone-sensitive lipase (HSL) and carnitine palmitoyltransferase-1 (CPT-1) significantly diminished. Peroxisome proliferator-activated receptor γ, sterol regulatory element-binding protein 1, stearoyl-CoA desaturase, adipocyte-fatty acid-binding proteins, ACC, LPL, and FAS gene or protein expression significantly increased by dietary energy increasing, whereas HSL, CPT-1, and GH gene or protein expression significantly decreased. These results indicated that high dietary energy promoting IMF deposition is mainly by downregulating pituitary GH gene expression, decreasing serum GH concentration, increasing lipogenic genes levels of mRNA, enzyme activities and protein expression, and decreasing lipolytic genes levels of mRNA, enzyme activities, and protein expression.
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Affiliation(s)
- Haibo Zhang
- College of Life Science and Environmetal Resource, Yichun University, Yichun, China
| | - Weikun Guan
- College of Life Science and Environmetal Resource, Yichun University, Yichun, China
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29
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An B, Xia J, Chang T, Wang X, Miao J, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. Physiol Genomics 2018; 50:523-531. [DOI: 10.1152/physiolgenomics.00022.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.
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Affiliation(s)
- Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xiaoqiao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jian Miao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
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Fatty acid profile and carcass traits of feedlot Nellore cattle fed crude glycerin and virginiamycin. Meat Sci 2018. [DOI: 10.1016/j.meatsci.2018.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Kawaguchi F, Kigoshi H, Nakajima A, Matsumoto Y, Uemoto Y, Fukushima M, Yoshida E, Iwamoto E, Akiyama T, Kohama N, Kobayashi E, Honda T, Oyama K, Mannen H, Sasazaki S. Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle. Anim Sci J 2018; 89:1060-1066. [DOI: 10.1111/asj.13035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/22/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Hiroto Kigoshi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Ayaka Nakajima
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yuta Matsumoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yoshinobu Uemoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Tohoku University; Sendai Japan
| | - Moriyuki Fukushima
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Emi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Takayuki Akiyama
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Namiko Kohama
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Eiji Kobayashi
- Division of Animal Breeding and Reproduction Research; Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Japan
| | - Takeshi Honda
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Kenji Oyama
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
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Lee JY, Ha J, Yi J, Jang J, Lee W, Lee Y, Oh DY, Han K. Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle. Genes Genomics 2018; 40:945-954. [PMID: 30155709 DOI: 10.1007/s13258-018-0704-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/30/2018] [Indexed: 11/28/2022]
Abstract
The fatty acid composition of adipose tissue in livestock has been recognized as an important carcass trait that affects meat quality. To determine the overall positive effect on fatty acid synthesis, we investigated PPARγ, SREBPs, FABP4, SCD, and FASN genes because SNP and/or SNP combinations were strongly affecting each fatty acid synthesis pathway. We screened their SNPs, SNP combinations, and genotype. Furthermore, we studied the economic traits C18:1, monounsaturated fatty acid (MUFA), and marbling score (MS). To enhance the accuracy of the predictive genetic effect, we applied a statistical adjustment model excluding environmental factors. We also selected superior genes, gene combinations, and genotypes for each economic trait by using multifactor dimensionality reduction. Based on the results, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.10153 A>G, g.3977-325 T>C) (AACC, AGCC, GGCC), (g.3690 G>A, g.3977-325 T>C) (GGCC, GACC), (g.3977-325 T>C, g.25670 C>T) (CCCC, CCCT, CCTT) (genotypes of the best SNP combination) was selected as the best gene combination for C18:1 and MUFA. In addition, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.3977-325 T>C, g.6974 G>A) (TTAA, CTAA, CCAA, CCGA, CCGG) as the best SNP combination for MS. We integrated genes that were selected as excellent SNP and SNP combinations affecting two main routes of the fatty acid synthesis pathway and identified the best and final SNP, SNP combination, and superior genotype.
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Affiliation(s)
- Jea-Young Lee
- Department of Statistics, Yeungnam University, Gyeongsan-si, Gyeongbuk, 38541, Republic of Korea
| | - Jaejung Ha
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Junkoo Yi
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Jieun Jang
- Department of Statistics, Yeungnam University, Gyeongsan-si, Gyeongbuk, 38541, Republic of Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yoonseok Lee
- Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea
| | - Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea.
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
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Raza SHA, Gui L, Khan R, Schreurs NM, Xiaoyu W, Wu S, Mei C, Wang L, Ma X, Wei D, Guo H, Zhang S, Wang X, Kaleri HA, Zan L. Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle. Gene 2017; 645:55-59. [PMID: 29273553 DOI: 10.1016/j.gene.2017.12.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/18/2017] [Indexed: 11/18/2022]
Abstract
Fatty acid synthase (FASN) is an enzyme involved with fat deposition and fatty acid composition in cattle. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with ultrasound carcass traits in order to assess the potential use of the FASN gene for the breeding selection of Qinchuan cattle for desirable carcass traits. The frequencies of SNP g.12740C>T, g.13192T>C and g.13232C>T were identified in 525 individual Qinchuan cattle which were also assessed for backfat depth, eye muscle area and intramuscular fat by ultrasound. According to the PIC values, g.13192T>C possessed an intermediate polymorphism (0.25<PIC<0.5). The SNPs of g.13232C>T, g.12740C>T possessed low polymorphism (PIC<0.25). Chi-square tests showed that g.13192T>C were in Hardy-Weinberg disequilibrium (c2<c0.052). Two SNPs were found to be associated with variation in ultrasound carcass traits. The H2H2 diplotypes had a greater back fat depth than H1H1, H1H4 and H1H2 (P<0.01). The TT genotype at g.13192T>C was associated with a greater eye muscle area and the TT genotype at g.13232C>T was associated with greater intramuscular fat. When these genotypes were combined there was no difference in eye muscle area and intramuscular fat between the diplotypes. The H2H2 diplotype was associated with carcass traits that are likely to provide economic advantage in Qinchuan cattle. Variations in the FASN genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Nicola M Schreurs
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Wang Xiaoyu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Sen Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xueyao Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dawei Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xingping Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hubdar Ali Kaleri
- Department of Animal Science and Aquaculture, Dalhousie University, Canada
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China.
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Ekine-Dzivenu C, Vinsky M, Basarab JA, Aalhus JL, Dugan MER, Li C. Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle. J Anim Sci 2017; 95:5184-5196. [PMID: 29293784 PMCID: PMC6292258 DOI: 10.2527/jas2017.1966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/20/2017] [Indexed: 01/11/2023] Open
Abstract
Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.
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Oh DY, Nam I, Hwang S, Kong H, Lee H, Ha J, Baik M, Oh MH, Kim S, Han K, Lee Y. In vivo evidence on the functional variation within fatty acid synthase gene associated with lipid metabolism in bovine longissimus dorsi muscle tissue. Genes Genomics 2017; 40:289-294. [PMID: 29892799 DOI: 10.1007/s13258-017-0634-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022]
Abstract
In Korean cattle, intramuscular fat (IMF), or marbling, of the longissimus dorsi muscle (LM) cross section is one of the most important indicators of beef quality and are influenced by environmental and genetic factors. This study was to evaluate the effect of SNPs on the beef quality in Korean cattle for functional studies, such as site-directed mutagenesis based on bovine adipocytes. The fatty acid synthase (FASN) gene plays an important role in lipogenesis. FASN is an essential metabolic and multifunctional enzyme in fatty acid synthesis. Several studies have reported that SNPs g.841G, g.16024A, g.16039T, and g.17924G have a significant impact on marbling scores in Korean cattle and Japanese Black cattle population. These SNPs are located in transcription factor binding sites, the beta-ketoacyl reductase, and thioesterase domains. Our results revealed that the g.17924 A>G SNP is located in the thioesterase domain of the FASN protein, and changes from polar, neutral, and hydrophilic to nonpolar, aliphatic, and hydrophobic, respectively. In in vivo LM tissue of Korean cattle, the g.17924A>G SNP has an effect on increasing fat deposition. Therefore, g.17924A>G SNP could be a causal mutation for increasing fat deposition in Korean cattle LM tissue.
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Affiliation(s)
- Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Insik Nam
- Research Center for Environment Friendly and Quality Livestock Production Technology, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea
| | - Sehwan Hwang
- Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea
| | - Hongsik Kong
- Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea
| | - Honggu Lee
- Department of Animal Science and Technology, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaejung Ha
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea
| | - Myunggi Baik
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Songmi Kim
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea. .,BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Yoonseok Lee
- Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea.
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Komatsu M, Nishino K, Fujimori Y, Haga Y, Iwama N, Arakawa A, Aihara Y, Takeda H, Takahashi H. Epistatic effects between pairs of the growth hormone secretagogue receptor 1a, growth hormone, growth hormone receptor, non-SMC condensin I complex, subunit G and stearoyl-CoA desaturase genes on carcass, price-related and fatty acid composition traits in Japanese Black cattle. Anim Sci J 2017; 89:273-288. [PMID: 29154485 DOI: 10.1111/asj.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 01/11/2023]
Abstract
Growth hormone secretagogue receptor 1a (GHSR1a), growth hormone (GH), growth hormone receptor (GHR), non-SMC condensin I complex, subunit G (NCAPG) and stearoyl-CoA desaturase (SCD), are known to play important roles in growth and lipid metabolisms. Single and epistatic effects of the five genes on carcass, price-related and fatty acid (FA) composition traits were analyzed in a commercial Japanese Black cattle population of Ibaraki Prefecture. A total of 650 steers and 116 heifers for carcass and price-related traits, and 158 steers for FA composition traits were used in this study. Epistatic effects between pairs of the five genes were found in several traits. Alleles showing strain-specific differences in the five genes had significant single and epistatic effects in some traits. The data suggest that a TG-repeat polymorphism of the GHSR1a.5'UTR-(TG)n locus plays a central role in gene-gene epistatic interaction of FA composition traits in the adipose tissue of Japanese Black cattle.
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Affiliation(s)
- Masanori Komatsu
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan.,Komatsu Laboratory of Computational Biology for Domestic Animals, Ryugasaki, Ibaraki, Japan
| | - Kagetomo Nishino
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan
| | - Yuki Fujimori
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Nagano Animal Industry Experiment Station, Shiojiri, Nagano, Japan
| | - Yasutoshi Haga
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Ibaraki Prefecture Agricultural College, Tsuchiura, Ibaraki, Japan
| | - Nagako Iwama
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Ibaraki Prefecture Ken-nan Livestock Office of Agriculture and Forestry, Tsuchiura, Ibaraki, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yoshito Aihara
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan
| | - Hisato Takeda
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hideaki Takahashi
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
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Genetics of Marbling in Wagyu Revealed by the Melting Temperature of Intramuscular and Subcutaneous Lipids. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2017; 2017:3948408. [PMID: 29201894 PMCID: PMC5672612 DOI: 10.1155/2017/3948408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/23/2017] [Accepted: 09/13/2017] [Indexed: 11/30/2022]
Abstract
Extreme marbling or intramuscular deposition of lipid is associated with Wagyu breeds and is therefore assumed to be largely inherited. However, even within 100% full blood Wagyu prepared under standard conditions, there is unpredictable scatter of the degree of marbling. Here, we evaluate melting temperature (Tm) of intramuscular fat as an alternative to visual scores of marbling. We show that “long fed” Wagyu generally has Tm below body temperature but with a considerable range under standardized conditions. Individual sires have a major impact indicating that the variation is genetic rather than environmental or random error. In order to measure differences of lower marbling breeds and at shorter feeding periods, we have compared Tm in subcutaneous fat samples from over the striploin. Supplementary feeding for 100 to 150 days leads to a rapid decrease in Tm of 50% Red Wagyu (Akaushi) : 50% European crosses, when compared to 100% European. This improvement indicates that the genetic effect of Wagyu is useful, predictable, and highly penetrant. Contemporaneous DNA extraction does not affect the measurement of Tm. Thus, provenance can be traced and substitution can be eliminated in a simple and cost-effective manner.
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Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PLoS One 2017; 12:e0183921. [PMID: 28841720 PMCID: PMC5571935 DOI: 10.1371/journal.pone.0183921] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/10/2017] [Indexed: 12/01/2022] Open
Abstract
Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp) were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV) were identified by aligning Nanyang to Qinchuan genome, 783 of which (27%) encompassed the coding regions of 495 functional genes. The gene ontology (GO) analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR) overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio) = -2.34988; P value = 1.53E-102). Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs, indels and CNV.
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Lloyd SS, Steele EJ, Valenzuela JL, Dawkins RL. Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic with Human Muscular Dystrophy. Int J Genomics 2017; 2017:6532837. [PMID: 28913347 PMCID: PMC5585636 DOI: 10.1155/2017/6532837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023] Open
Abstract
Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping. Fortunately, for the production of healthy beef, some of these haplotypes are sufficiently penetrant to be expressed in heterozygous crossbreds, thereby allowing selection of sires which will improve the healthiness of beef produced under even harsh climatic conditions. The region of Bota 19 is syntenic to a region of Hosa 17 known to be important in muscle metabolism and in determining susceptibility to a form of human muscular dystrophy.
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Affiliation(s)
- Sally S. Lloyd
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward J. Steele
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
| | - Jose L. Valenzuela
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
| | - Roger L. Dawkins
- CY O'Connor ERADE Village Foundation, P.O. Box 5100, Canning Vale South, WA 6155, Australia
- Melaleuka Stud, 24 Genomics Rise, Piara Waters, WA 6112, Australia
- Centre for Innovation in Agriculture, Murdoch University, Murdoch, WA 6150, Australia
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40
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Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle. Sci Rep 2017; 7:5278. [PMID: 28706200 PMCID: PMC5509646 DOI: 10.1038/s41598-017-05702-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/01/2017] [Indexed: 11/22/2022] Open
Abstract
Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified. Gene Ontology and KEGG pathway analysis revealed that many differentially expressed genes were enriched in several biological processes and pathways relevant to adipogenesis and lipid metabolism, in which PPAR and fatty acid metabolism signaling pathways with related genes such as PPARγ, PLIN2 and ELOVL6 et al. play a critical role. Protein-protein interaction network analysis showed EGR1, FOS, SERPINE1, AGT, MMP2 may have great impact on adipocyte differentiation and adipogenesis. Moreover, potential alternative splicing events and single nucleotide polymorphisms (SNPs) were also identified. In summary, we comprehensively analyzed and discussed the transcriptome of subcutaneous adipose tissue of Wagyu and Holstein cattle, which might provide a theoretical basis for better understanding molecular mechanism of fat metabolism and deposition in beef cattle.
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Association of the calpastatin genotypes, haplotypes, and SNPs with meat quality and fatty acid composition in two Iranian fat- and thin-tailed sheep breeds. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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42
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Oh DY, Lee JY, Jang JE, Lee SU. Genetic effects of sterol regulatory element binding proteins and fatty acid-binding protein4 on the fatty acid composition of Korean cattle (Hanwoo). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:160-166. [PMID: 27492349 PMCID: PMC5205601 DOI: 10.5713/ajas.16.0262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/25/2016] [Accepted: 08/03/2016] [Indexed: 11/27/2022]
Abstract
Objective This study identifies single-nucleotide polymorphisms (SNP) or gene combinations that affect the flavor and quality of Korean cattle (Hanwoo) by using the SNP Harvester method. Methods Four economic traits (oleic acid [C18:1], saturated fatty acids), monounsaturated fatty acids, and marbling score) were adjusted for environmental factors in order to focus solely on genetic effects. The SNP Harvester method was used to investigate gene combinations (two-way gene interactions) associated with these economic traits. Further, a multifactor dimensionality reduction method was used to identify superior genotypes in gene combinations. Results Table 3 to 4 show the analysis results for differences between superior genotypes and others for selected major gene combinations using the multifactor dimensionality reduction method. Environmental factors were adjusted for in order to evaluate only the genetic effect. Table 5 shows the adjustment effect by comparing the accuracy before and after correction in two-way gene interactions. Conclusion The g.3977-325 T>C and (g.2988 A>G, g.3977-325 T>C) combinations of fatty acid-binding protein4 were the superior gene, and the superior genotype combinations across all economic traits were the CC genotype at g.3977-325 T>C and the AACC, GACC, GGCC genotypes of (g.2988 A>G, g.3977-325 T>C).
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Affiliation(s)
- Dong-Yep Oh
- Livestock Research institute, Yeongju 750-871, Korea
| | - Jea-Young Lee
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Ji-Eun Jang
- Department of Statistics, Yeungnam University, Gyeongsan 712-749, Korea
| | - Seung-Uk Lee
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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Jomane FN, Ishida T, Tokunaga T, Morita T. Variations in genes involved in fat metabolism and their association with ultrasonic and carcass traits in Japanese Black steers. Anim Sci J 2016; 88:413-420. [PMID: 27417411 DOI: 10.1111/asj.12650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/08/2016] [Accepted: 04/07/2016] [Indexed: 11/27/2022]
Abstract
Polymorphisms in genes involved in lipid metabolism have been reported to be associated with fatty acid composition of adipose tissue. However, the relationship of these polymorphisms with premortem ultrasonic traits is unknown. The objective of this study, therefore, was to assess the association between polymorphisms in fatty acid synthase, stearoyl-coenzyme A desaturase (SCD), sterol regulatory element-binding protein 1 (SREBP1), diacylglycerol acyltransferase 1, and nuclear receptor subfamily 1, group H, number 3 genes with ultrasonic and carcass traits in Japanese Black steers (n = 300) under progeny testing at the Livestock Improvement Association of Miyazaki. To have a comprehensive analysis of the association between the aforementioned genetic polymorphisms and ultrasonic traits, longitudinal measurements of ultrasonic traits were taken. Furthermore, the association of these genetic polymorphisms and carcass traits was evaluated. The polymorphisms in the SCD gene and SREBP1 were associated (P < 0.05) with some ultrasonic traits at multiple stages. To add to that, the polymorphisms were associated (P < 0.05) with some carcass traits. These findings suggest that the polymorphisms in SCD and SREBP1 are functional mutations or could be related to mutations that can aid in selection to improve some ultrasonic and carcass traits.
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Affiliation(s)
- Fortune N Jomane
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Takafumi Ishida
- Department of Animal and Grassland Sciences, University of Miyazaki, Miyazaki, Japan
| | - Tadaaki Tokunaga
- Department of Animal and Grassland Sciences, University of Miyazaki, Miyazaki, Japan
| | - Tetsuo Morita
- Department of Animal and Grassland Sciences, University of Miyazaki, Miyazaki, Japan
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Aali M, Moradi-Shahrbabak H, Moradi-Shahrbabak M, Sadeghi M, Kohram H. Polymorphism in the SCD gene is associated with meat quality and fatty acid composition in Iranian fat- and thin-tailed sheep breeds. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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45
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Sasago N, Abe T, Sakuma H, Kojima T, Uemoto Y. Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle. Anim Sci J 2016; 88:33-44. [PMID: 27112906 DOI: 10.1111/asj.12595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/18/2015] [Accepted: 11/30/2016] [Indexed: 11/29/2022]
Abstract
We performed a genome-wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non-CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW-related genes and two fatty acid-related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW-related genes associated with the rib-eye area and fatty acid composition were identified, and fatty acid-related genes had no relationship with other traits. Moreover, the favorable allele of CW-related genes had an unfavorable effect on fatty acid composition.
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Affiliation(s)
- Nanae Sasago
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Tsuyoshi Abe
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Hironori Sakuma
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
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Growth, carcass and meat quality traits in beef from Angus, Hereford and cross-breed grazing steers, and their association with SNPs in genes related to fat deposition metabolism. Meat Sci 2016; 114:121-129. [DOI: 10.1016/j.meatsci.2015.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
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47
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Bartoň L, Bureš D, Kott T, Řehák D. Associations of polymorphisms in bovine DGAT1, FABP4, FASN, and PPARGC1A genes with intramuscular fat content and the fatty acid composition of muscle and subcutaneous fat in Fleckvieh bulls. Meat Sci 2016; 114:18-23. [DOI: 10.1016/j.meatsci.2015.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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48
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Yonekura S, Hirota S, Miyazaki H, Tokutake Y. Subcellular Localization and Polymorphism of Bovine FABP4 in Bovine Intramuscular Adipocytes. Anim Biotechnol 2016; 27:96-103. [DOI: 10.1080/10495398.2015.1102148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Buchanan JW, Reecy JM, Garrick DJ, Duan Q, Beitz DC, Mateescu RG. Genetic parameters and genetic correlations among triacylglycerol and phospholipid fractions in Angus cattle. J Anim Sci 2016; 93:522-8. [PMID: 26020741 DOI: 10.2527/jas.2014-8418] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The objective of this study was to estimate genetic parameters for intramuscular fatty acids from triacylglycerol (TAG) and phospholipid (PL) fractions in beef LM tissue. Longissimus muscle samples were obtained from 1,833 Angus cattle to determine the intramuscular fatty acid composition for 31 lipids and lipid classes from TAG and PL fractions and were classified by structure into saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (n-3), and omega-6 (n-6) fatty acids. An atherogenic index (AI) was also determined as a measure of the unsaturated fatty acid to SFA ratio. Restricted maximum likelihood methods combined with pedigree data were used to estimate variance components with the WOMBAT software package. Heritability estimates ranged from 0.00 to 0.63 for the major classes of fatty acids. Heritability estimates differed between the TAG and PL fractions, with higher estimates for TAG up to 0.64 and lower estimates for PL that ranged from 0.00 to 0.14. Phenotypic and genetic correlations among individual fatty acids were determined for the TAG fraction as well as among carcass traits, including rib eye area, numerical marbling score, yield grade, ether fat, and Warner-Bratzler shear force value. Strong negative or positive genetic correlations were observed among individual fatty acids in the TAG fraction, which ranged from -0.99 to 0.97 ( < 0.05). Moderate correlations between carcass traits and fatty acids from the TAG fraction ranged from -0.43 to 0.32 ( < 0.05). These results indicate that fatty acids prominent in beef tissues show significant genetic variation as well as genetic relationships with carcass traits.
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50
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Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds. ACTA VET BRNO 2015. [DOI: 10.2754/avb201584040327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this study was to evaluate the polymorphic effects of two single nucleotide polymorphisms (SNPs) of fatty acid binding protein (FABP4) and stearoyl-CoA desaturase (SCD) genes on intramuscular fatty acid profiles in the longissimus muscle in two cattle breeds. Two previously reported SNPs of bovine FABP4 (7516G>C) and SCD (878C>T) were in turn assessed for their associations with intramuscular fatty acid profiles from the upper sirloin cuts of Aberdeen Angus and Blonde d’Aquitaine cattle. In total, 33 animals were genotyped using PCR-RFLP. Intramuscular fatty acid composition was evaluated using two complementary statistical approaches: a classical univariate regression model and a multivariate approach using a combination of Principal Component Analysis and Random Forests. Significant effect of FABP4 SNP genotypes was found for several fatty acids including C15:0, C17:0, C18:0, C14:1, C17:1, C18:2n6, C20:4n6, C20:5n3, C22:5n3, total n-3, n-6 and total SFA (P < 0.05). These results suggest that FABP4 is a potential candidate gene affecting fatty acid composition in beef cattle.
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