Use of molecular markers to improve relationship information in the genetic evaluation of beef cattle tick resistance under pedigree‐based models. (22nd September 2016)

• Record Type: Journal Article
• Authors: Junqueira, V.S.; Cardoso, F.F.; Oliveira, M.M.; Sollero, B.P.; Silva, F.F.; Lopes, P.S.
• Is Part Of: Journal of animal breeding and genetics. Volume 134:Number 1(2017)
• Page Start: 14
• Page End: 26
• Publication Date: 2016-09-22
• Subjects: Accuracy -- beef cattle -- numerator relationship matrix -- SNPs; Livestock -- Breeding -- Periodicals; Livestock -- Genetics -- Periodicals; 636.0820
• DOI: 10.1111/jbg.12239
• Languages: English
• ISSNs: 0931-2668

Abstract

Summary: 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.