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Selionova M, Trukhachev V, Aibazov M, Sermyagin A, Belous A, Gladkikh M, Zinovieva N. Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals (Basel) 2024; 14:327. [PMID: 38275787 PMCID: PMC10812594 DOI: 10.3390/ani14020327] [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: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number-only 1 SNP-for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Vladimir Trukhachev
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Magomet Aibazov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Marianna Gladkikh
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
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Salgado Pardo JI, Delgado Bermejo JV, González Ariza A, León Jurado JM, Marín Navas C, Iglesias Pastrana C, Martínez Martínez MDA, Navas González FJ. Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats ( Capra hircus). Animals (Basel) 2022; 12:ani12080988. [PMID: 35454235 PMCID: PMC9026325 DOI: 10.3390/ani12080988] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content). Abstract Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.
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Affiliation(s)
- Jose Ignacio Salgado Pardo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - José Manuel León Jurado
- Agropecuary Provincial Center of Córdoba, Provincial Council of Córdoba, 14014 Córdoba, Spain;
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Carlos Iglesias Pastrana
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain
- Correspondence: ; Tel.: +34-63-853-5046 (ext. 621262)
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Inostroza MGP, González FJN, Landi V, Jurado JML, Bermejo JVD, Fernández Álvarez J, Martínez Martínez MDA. Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats. Animals (Basel) 2020; 10:E1845. [PMID: 33050522 PMCID: PMC7600415 DOI: 10.3390/ani10101845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 01/05/2023] Open
Abstract
Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats.
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Affiliation(s)
- María Gabriela Pizarro Inostroza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
- Animal Breeding Consulting, S.L., Córdoba Science and Technology Park Rabanales 21, 14071 Córdoba, Spain
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Valenzano, Italy;
| | - Jose Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, Córdoba, 14071 Córdoba, Spain;
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
| | - Javier Fernández Álvarez
- National Association of Breeders of Murciano-Granadina Goat Breed, Fuente Vaqueros, 18340 Granada, Spain;
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
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Pizarro Inostroza MG, Landi V, Navas González FJ, León Jurado JM, Delgado Bermejo JV, Fernández Álvarez J, Martínez Martínez MDA. Integrating Casein Complex SNPs Additive, Dominance and Epistatic Effects on Genetic Parameters and Breeding Values Estimation for Murciano-Granadina Goat Milk Yield and Components. Genes (Basel) 2020; 11:E309. [PMID: 32183253 PMCID: PMC7140789 DOI: 10.3390/genes11030309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/12/2020] [Indexed: 11/23/2022] Open
Abstract
Assessing dominance and additive effects of casein complex single-nucleotide polymorphisms (SNPs) (αS1, αS2, β, and κ casein), and their epistatic relationships may maximize our knowledge on the genetic regulation of profitable traits. Contextually, new genomic selection perspectives may translate this higher efficiency into higher accuracies for milk yield and components' genetic parameters and breeding values. A total of 2594 lactation records were collected from 159 Murciano-Granadina goats (2005-2018), genotyped for 48 casein loci-located SNPs. Bonferroni-corrected nonparametric tests, categorical principal component analysis (CATPCA), and nonlinear canonical correlations were performed to quantify additive, dominance, and interSNP epistatic effects and evaluate the outcomes of their inclusion in quantitative and qualitative milk production traits' genetic models (yield, protein, fat, solids, and lactose contents and somatic cells count). Milk yield, lactose, and somatic cell count heritabilities increased considerably when the model including genetic effects was considered (0.46, 0.30, 0.43, respectively). Components standard prediction errors decreased, and accuracies and reliabilities increased when genetic effects were considered. Conclusively, including genetic effects and relationships among these heritable biomarkers may improve model efficiency, genetic parameters, and breeding values for milk yield and composition, optimizing selection practices profitability for components whose technological application may be especially relevant for the cheese-making dairy sector.
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Affiliation(s)
- María Gabriela Pizarro Inostroza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
- Animal Breeding Consulting, S.L., Córdoba Science and Technology Park Rabanales 21, 14071 Córdoba, Spain
| | - Vincenzo Landi
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Valenzano, Italy;
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
| | - Jose Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, Córdoba, 14071 Córdoba, Spain;
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
| | - Javier Fernández Álvarez
- National Association of Breeders of Murciano-Granadina Goat Breed, Fuente Vaqueros, 18340 Granada, Spain;
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (M.G.P.I.); (J.V.D.B.); (M.d.A.M.M.)
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Pizarro Inostroza MG, Landi V, Navas González FJ, León Jurado JM, Martínez Martínez MDA, Fernández Álvarez J, Delgado Bermejo JV. Non-parametric association analysis of additive and dominance effects of casein complex SNPs on milk content and quality in Murciano-Granadina goats. J Anim Breed Genet 2019; 137:407-422. [PMID: 31743943 DOI: 10.1111/jbg.12457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/06/2019] [Accepted: 10/28/2019] [Indexed: 11/26/2022]
Abstract
Goat milk casein proteins (αS1, αS2, β and κ) are encoded by four loci (CSN1S1, CSN1S2, CSN2 and CSN3, respectively) clustered within 250 kb in chromosome 6. In this study, 159 Murciano-Granadina goats were genotyped for 48 SNPs within the entire casein region. Phenotypes on milk yield and components were obtained from 2,594 dairy registries. Additive and dominance effects on milk composition and quality were studied using non-parametric tests and principal component analysis to prevent SNPs multicollinearity. Two deletions in exon 4 (CSN1S1 and CSN3), one in exon 7 (CSN2) and one in exon 15 (CSN1S2) have been found at frequencies ranging from 0.12 to 0.50. Bonferroni-corrected significant SNP additive and dominance effects were found for milk yield, fat, protein, dry matter and lactose, and somatic cells. Exons 15 and 7 were significantly associated with milk yield and components except for lactose and somatic cells, while exon 4 was significantly associated with milk yield and components except for protein and dry matter. SNPs' associations with somatic cells were less frequent and weaker than those with milk yield and components. As caseins increase, somatic cells decrease, reducing milk enzymatic activity and consumption suitability. Hence, including molecular information in breeding schemes may promote production efficiency, as selecting against undesirable alleles could prevent the compromises derived from their dominance effects.
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Affiliation(s)
| | - Vincenzo Landi
- Animal Breeding Consulting SL, Córdoba Science and Technology Park, Córdoba, Spain
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Inglingstad R, Skeie S, Vegarud G, Devold T, Chilliard Y, Eknæs M. Feeding a concentrate rich in rapeseed oil improves fatty acid composition and flavor in Norwegian goat milk. J Dairy Sci 2017; 100:7088-7105. [DOI: 10.3168/jds.2016-12383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/15/2017] [Indexed: 11/19/2022]
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Pegolo S, Cecchinato A, Mele M, Conte G, Schiavon S, Bittante G. Effects of candidate gene polymorphisms on the detailed fatty acids profile determined by gas chromatography in bovine milk. J Dairy Sci 2016; 99:4558-4573. [DOI: 10.3168/jds.2015-10420] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/10/2016] [Indexed: 11/19/2022]
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Silanikove N. Selected lectures from the Regional IGA Conference on Goat Milk Quality, Tromsø, Norway, June 4–6, 2013: From the Editor bird-eye. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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