title: Use of molecular markers to improve relationship information in the genetic evaluation of beef cattle tick resistance under pedigree-based models.
abstract: The selection of genetically superior individuals is conditional upon accurate breeding value predictions which, in turn, are highly depend on how precisely relationship is represented by pedigree. For that purpose, the numerator relationship matrix is essential as a priori information in mixed model equations. The presence of pedigree errors and/or the lack of relationship information affect the genetic gain because it reduces the correlation between the true and estimated breeding values. Thus, this study aimed to evaluate the effects of correcting the pedigree relationships using single-nucleotide polymorphism (SNP) markers on genetic evaluation accuracies for resistance of beef cattle to ticks. Tick count data from Hereford and Braford cattle breeds were used as phenotype. Genotyping was carried out using a high-density panel (BovineHD - Illumina®bead chip with 777 962 SNPs) for sires and the Illumina BovineSNP50 panel (54 609 SNPs) for their progenies. The relationship between the parents and progenies of genotyped animals was evaluated, and mismatches were based on the Mendelian conflicts counts. Variance components and genetic parameters estimates were obtained using a Bayesian approach via Gibbs sampling, and the breeding values were predicted assuming a repeatability model. A total of 460 corrections in relationship definitions were made (Table 1) corresponding to 1018 (9.5%) tick count records. Among these changes, 97.17% (447) were related to the sire's information, and 2.8% (13) were related to the dam's information. We observed 27.2% (236/868) of Mendelian conflicts for sire-progeny genotyped pairs and 14.3% (13/91) for dam-progeny genotyped pairs. We performed 2174 new definitions of half-siblings according to the correlation coefficient between the coancestry and molecular coancestry matrices. It was observed that higher-quality genetic relationships did not result in significant differences of variance components estimates; however, they resulted in more accurate breeding values predictions. Using SNPs to assess conflicts between parents and progenies increases certainty in relationships and consequently the accuracy of breeding value predictions of candidate animals for selection. Thus, higher genetic gains are expected when compared to the traditional non-corrected relationship matrix.
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais (MG), Brazil.
authors.forename: V S
authors.initials: VS
authors.lastname: Junqueira
authors.affiliation: Empresa Brasileira de Pesquisa Agropecuária, Centro de Pesquisa de Pecuária dos Campos Sul-Brasileiros, Bagé, Rio Grande do Sul (RS), Brazil.|Departamento de Zootecnia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul (RS), Brazil.
authors.forename: F F
authors.initials: FF
authors.lastname: Cardoso
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Santa Maria, Rio Grande do Sul (RS), Brazil.
authors.forename: M M
authors.initials: MM
authors.lastname: Oliveira
authors.affiliation: Empresa Brasileira de Pesquisa Agropecuária, Centro de Pesquisa de Pecuária dos Campos Sul-Brasileiros, Bagé, Rio Grande do Sul (RS), Brazil.
authors.forename: B P
authors.initials: BP
authors.lastname: Sollero
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais (MG), Brazil.
authors.forename: F F
authors.initials: FF
authors.lastname: Silva
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Minas Gerais (MG), Brazil.
authors.forename: P S
authors.initials: PS
authors.lastname: Lopes
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics* / Q000276:immunology* / Q000469:parasitology; D004478:Ectoparasitic Infestations / Q000235:genetics / Q000276:immunology; D005260:Female; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D048494:Rhipicephalus / Q000502:physiology
keywords: Accuracy; SNPs; beef cattle; numerator relationship matrix