J Anim Breed Genet. 2019;00:1–16. wileyonlinelibrary.com/journal/jbg | 1 © 2019 Blackwell Verlag GmbH 1 | INTRODUCTION Worldwide exportations of Spanish native Murciano- Granadina goats have increased during the last decades, given the high ability of the breed to adapt to very diverse systems (Delgado et al., 2017). Consequently, the economical repercussion of Murciano-Granadina breed's milk, the main ingredient for the manufacture of fresh, semi-aged and aged cheeses with denomination of origin (Cheese of Murcia), has experienced a remarkable increase. Received: 20 August 2019 | Revised: 6 October 2019 | Accepted: 28 October 2019 DOI: 10.1111/jbg.12457 ORIGINAL ARTICLE Non-parametric association analysis of additive and dominance effects of casein complex SNPs on milk content and quality in Murciano-Granadina goats María Gabriela Pizarro Inostroza 1 | Vincenzo Landi 2 | Francisco Javier Navas González 1 | José Manuel León Jurado 3 | María del Amparo Martínez Martínez 2 | Javier Fernández Álvarez 4 | Juan Vicente Delgado Bermejo 1 1 Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain 2 Animal Breeding Consulting SL, Córdoba Science and Technology Park, Córdoba, Spain 3 Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, Córdoba, Spain 4 National Association of Breeders of Murciano-Granadina Goat Breed, Granada, Spain Correspondence Francisco Javier Navas González, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba 14071, Spain. Email: fjng87@hotmail.com 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 rang- ing 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 com- ponents. As caseins increase, somatic cells decrease, reducing milk enzymatic activ- ity 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. KEYWORDS associations, caseins, non-parametric tools, snps, somatic cells