|
1
|
Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, Malau-Aduli AEO. Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb. Foods 2021; 10:foods10102288. [PMID: 34681337 PMCID: PMC8535056 DOI: 10.3390/foods10102288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/14/2023] Open
Abstract
Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.
Collapse
Affiliation(s)
- Shedrach Benjamin 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- National Veterinary Research Institute, Private Mail Bag 01 Vom, Plateau State, Nigeria
| | - John Roger 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan;
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Alyssa Maree Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Felista Waithira 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Richard Crawford Edmunds
- 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | | | - Michelle Lauren Elizabeth Henry
- Gundagai Meat Processors, 2916 Gocup Road, South Gundagai, NSW 2722, Australia;
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert Tumwesigye 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Oyelola Abdulwasiu 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 Enoch Othniel 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; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- Correspondence: ; Tel.: +61-747-815-339
| |
Collapse
|
|
2
|
Marina H, Reverter A, Gutiérrez-Gil B, Alexandre PA, Porto-Neto LR, Suárez-Vega A, Li Y, Esteban-Blanco C, Arranz JJ. Gene Networks Driving Genetic Variation in Milk and Cheese-Making Traits of Spanish Assaf Sheep. Genes (Basel) 2020; 11:genes11070715. [PMID: 32605032 PMCID: PMC7397207 DOI: 10.3390/genes11070715] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 02/04/2023] Open
Abstract
Most of the milk produced by sheep is used for the production of high-quality cheese. Consequently, traits related to milk coagulation properties and cheese yield are economically important to the Spanish dairy industry. The present study aims to identify candidate genes and their regulators related to 14 milk and cheese-making traits and to develop a low-density panel of markers that could be used to predict an individual's genetic potential for cheese-making efficiency. In this study, we performed a combination of the classical genome-wide association study (GWAS) with a stepwise regression method and a pleiotropy analysis to determine the best combination of the variants located within the confidence intervals of the potential candidate genes that may explain the greatest genetic variance for milk and cheese-making traits. Two gene networks related to milk and cheese-making traits were created using the genomic relationship matrices built through a stepwise multiple regression approach. Several co-associated genes in these networks are involved in biological processes previously found to be associated with milk synthesis and cheese-making efficiency. The methodology applied in this study enabled the selection of a co-association network comprised of 374 variants located in the surrounding of genes showing a potential influence on milk synthesis and cheese-making efficiency.
Collapse
Affiliation(s)
- Héctor Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Yutao Li
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
- Correspondence: ; Tel.: +34-987-291-470
| |
Collapse
|
|
3
|
Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, Malau-Aduli AEO. Genetics of Omega-3 Long-Chain Polyunsaturated Fatty Acid Metabolism and Meat Eating Quality in Tattykeel Australian White Lambs. Genes (Basel) 2020; 11:E587. [PMID: 32466330 PMCID: PMC7288343 DOI: 10.3390/genes11050587] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022] Open
Abstract
Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and childhood brain functions, and include alpha linolenic (ALA), eicosapentaenoic (EPA), docosahexaenoic (DHA) and docosapentaenoic (DPA) acids. The primary objective of this review was to access, retrieve, synthesise and critically appraise the published literature on the synthesis, metabolism and genetics of n-3 LC-PUFA and meat eating quality. Studies on IMF content, FMP and fatty acid composition were reviewed to identify knowledge gaps that can inform future research with Tattykeel Australian White (TAW) lambs. The TAW is a new sheep breed exclusive to MARGRA brand of lamb with an outstanding low fat melting point (28-39°C), high n-3 LC-PUFA EPA+DHA content (33-69mg/100g), marbling (3.4-8.2%), tenderness (20.0-38.5N) and overall consumer liking (7.9-8.5). However, correlations between n-3 LC-PUFA profile, stearoyl-CoA desaturase (SCD), fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), other lipogenic genes and meat quality traits present major knowledge gaps. The review also identified research opportunities in nutrition-genetics interactions aimed at a greater understanding of the genetics of n-3 LC-PUFA, feedlot finishing performance, carcass traits and eating quality in the TAW sheep. It was concluded that studies on IMF, FMP and n-3 LC-PUFA profiles in parental and progeny generations of TAW sheep will be foundational for the genetic selection of healthy lamb eating qualities and provide useful insights into their correlations with SCD, FASN and FABP4 genes.
Collapse
Affiliation(s)
- Shedrach Benjamin 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- National Veterinary Research Institute, Private Mail Bag 01, Vom, Plateau State, Nigeria
| | - John Roger 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Roger Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia; (R.H.); (A.M.B.)
| | - Alyssa Maree Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia; (R.H.); (A.M.B.)
| | - Felista Waithira 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Richard Crawford Edmunds
- 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | | | - Michelle Lauren Elizabeth Henry
- Gundagai Meat Processors, 2916 Gocup Road, South Gundagai, New South Wales 2722, Australia;
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert Tumwesigye 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Oyelola Abdulwasiu Adegboye
- Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia;
| | - Aduli Enoch Othniel 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, Queensland 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| |
Collapse
|
|
4
|
Shishay G, Liu G, Jiang X, Yu Y, Teketay W, Du D, Jing H, Liu C. Variation in the Promoter Region of the MC4R Gene Elucidates the Association of Body Measurement Traits in Hu Sheep. Int J Mol Sci 2019; 20:E240. [PMID: 30634446 PMCID: PMC6358852 DOI: 10.3390/ijms20020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 12/30/2018] [Indexed: 12/15/2022] Open
Abstract
The melanocortin 4 receptor (MC4R) gene is expressed in the appetite-regulating areas of the brain and is engaged in the leptin signaling pathway. Although previous studies have identified variants in the coding region of the sheep MC4R gene showing significant associations with birth weight, weaning weight, and backfat thickness, no such associations have been reported for the promoter region. Besides, the essential promoter region of the sheep MC4R has not been delineated. In this study, to better understand the transcriptional regulation of MC4R and to elucidate the association between regulatory variants and haplotypes with body measurement traits in sheep, we cloned and characterized the MC4R promoter. We found that the minimal promoter of the gene is located within the region -1207/-880 bp upstream of the first exon. Real-time quantitative PCR (RT-qPCR) data revealed the mRNA expression of the MC4R gene had a significant difference between sex and age. In the association analysis, eight single nucleotide polymorphisms (SNPs) had a significant association with one or more traits (p < 0.05); of these, two SNPs were novel. Notably, individuals with haplotype H1H2 (CT-GA-GT-GA-GT-GA-GA-CG) were heavier in body weight than other haplotypes. Altogether, variations in the MC4R gene promoter, most notably haplotype H1H2, may greatly benefit marker-assisted selection in sheep.
Collapse
Affiliation(s)
- Girmay Shishay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Yu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wassie Teketay
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dandan Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huang Jing
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenghui Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|