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Zhang L, Duan Y, Zhao S, Xu N, Zhao Y. Caprine and Ovine Genomic Selection-Progress and Application. Animals (Basel) 2024; 14:2659. [PMID: 39335248 PMCID: PMC11428554 DOI: 10.3390/ani14182659] [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: 08/06/2024] [Revised: 08/28/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.
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Affiliation(s)
| | | | | | - Naiyi Xu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China; (L.Z.); (Y.D.); (S.Z.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China; (L.Z.); (Y.D.); (S.Z.)
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Becker GM, Thorne JW, Burke JM, Lewis RM, Notter DR, Morgan JLM, Schauer CS, Stewart WC, Redden RR, Murdoch BM. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genet Sel Evol 2024; 56:56. [PMID: 39080565 PMCID: PMC11290166 DOI: 10.1186/s12711-024-00905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/23/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
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Affiliation(s)
- Gabrielle M Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
| | - Jacob W Thorne
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David R Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Christopher S Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, USA
| | - Whit C Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - R R Redden
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA.
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Li W, Li W, Song Z, Gao Z, Xie K, Wang Y, Wang B, Hu J, Zhang Q, Ning C, Wang D, Fan X. Marker Density and Models to Improve the Accuracy of Genomic Selection for Growth and Slaughter Traits in Meat Rabbits. Genes (Basel) 2024; 15:454. [PMID: 38674388 PMCID: PMC11050255 DOI: 10.3390/genes15040454] [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: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The selection and breeding of good meat rabbit breeds are fundamental to their industrial development, and genomic selection (GS) can employ genomic information to make up for the shortcomings of traditional phenotype-based breeding methods. For the practical implementation of GS in meat rabbit breeding, it is necessary to assess different marker densities and GS models. Here, we obtained low-coverage whole-genome sequencing (lcWGS) data from 1515 meat rabbits (including parent herd and half-sibling offspring). The specific objectives were (1) to derive a baseline for heritability estimates and genomic predictions based on randomly selected marker densities and (2) to assess the accuracy of genomic predictions for single- and multiple-trait linear mixed models. We found that a marker density of 50 K can be used as a baseline for heritability estimation and genomic prediction. For GS, the multi-trait genomic best linear unbiased prediction (GBLUP) model results in more accurate predictions for virtually all traits compared to the single-trait model, with improvements greater than 15% for all of them, which may be attributed to the use of information on genetically related traits. In addition, we discovered a positive correlation between the performance of the multi-trait GBLUP and the genetic correlation between the traits. We anticipate that this approach will provide solutions for GS, as well as optimize breeding programs, in meat rabbits.
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Affiliation(s)
- Wenjie Li
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
- Department of Animal Genetics and Breeding, University of Anhui Agricultural, Hefei 230031, China
| | - Wenqiang Li
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Zichen Song
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Zihao Gao
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Kerui Xie
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Yubing Wang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Bo Wang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Jiaqing Hu
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Qin Zhang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Chao Ning
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Ministry of Agriculture and Rural Affairs, Taian 271000, China
| | - Xinzhong Fan
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
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Garzón A, Perea JM, Angón E, Ryan EG, Keane OM, Caballero-Villalobos J. Exploring Interrelationships between Colour, Composition, and Coagulation Traits of Milk from Cows, Goats, and Sheep. Foods 2024; 13:610. [PMID: 38397587 PMCID: PMC10887686 DOI: 10.3390/foods13040610] [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: 02/02/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
This study explores the interrelationships between the composition, coagulation, and colour of sheep, goat, and cow milk to identify their similarities and differences and to assess whether the relationships between the variables are common to all species or whether they emerge from species-specific relationships. For this purpose, 2400 individual milk samples were analysed. The differences and similarities between the species were determined using discriminant analysis and cluster analysis. The results show a clear differentiation between species. Sheep milk stands out for its cheesemaking capacity and shows similarities with goat milk in composition and coagulation. Nonetheless, colorimetry highlights a greater similarity between sheep and cow milk. Composition and colorimetry were more discriminating than coagulation, and the variables that differed the most were fat, protein, curd yield, lightness, and red-green balance. Using canonical correlation, the interrelationships between the different sets of variables were explored, revealing patterns of common variation and species-specific relationships. Colorimetric variables were closely related to milk solids in all species, while in sheep milk, an inverse relationship with lactose was also identified. Furthermore, a strong relationship was revealed for all species between colour and curd yield. This could be modelled and applied to estimate the technological value of milk, proving colorimetry as a useful tool for the dairy industry.
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Affiliation(s)
- Ana Garzón
- Department of Animal Production, University of Córdoba, 14071 Córdoba, Spain; (A.G.); (J.M.P.); (E.A.)
| | - José M. Perea
- Department of Animal Production, University of Córdoba, 14071 Córdoba, Spain; (A.G.); (J.M.P.); (E.A.)
| | - Elena Angón
- Department of Animal Production, University of Córdoba, 14071 Córdoba, Spain; (A.G.); (J.M.P.); (E.A.)
| | - Eoin G. Ryan
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, D04 V1W8 Belfield, Ireland;
| | - Orla M. Keane
- Teagasc Animal & Bioscience Research Department, Grange, C15 PW93 Dunsany, Co. Meath, Ireland;
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