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Integrating Casein Complex SNPs Additive, Dominance and Epistatic Effects on Genetic Parameters and Breeding Values Estimation for Murciano-Granadina Goat Milk Yield and Components

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Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain
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Animal Breeding Consulting, S.L., Córdoba Science and Technology Park Rabanales 21, 14071 Córdoba, Spain
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Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Valenzano, Italy
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Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, Córdoba, 14071 Córdoba, Spain
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National Association of Breeders of Murciano-Granadina Goat Breed, Fuente Vaqueros, 18340 Granada, Spain
*
Author to whom correspondence should be addressed.
Genes 2020, 11(3), 309; https://doi.org/10.3390/genes11030309
Received: 1 March 2020 / Accepted: 12 March 2020 / Published: 14 March 2020
(This article belongs to the Section Animal Genetics and Genomics)
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. View Full-Text
Keywords: OVERALS; CATPCA; Kruskal–Wallis; association; restricted maximum likelihood; linkage disequilibrium; casein complex; MTDFREML OVERALS; CATPCA; Kruskal–Wallis; association; restricted maximum likelihood; linkage disequilibrium; casein complex; MTDFREML
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Pizarro Inostroza, M.G.; Landi, V.; Navas González, F.J.; León Jurado, J.M.; Delgado Bermejo, J.V.; Fernández Álvarez, J.; Martínez Martínez, M.A. 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 2020, 11, 309.

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