Abstract
The aim of this study was to predict the genomic breeding value (DGV) of production, selected conformation and reproductive traits, and somatic cell score of dairy cattle in Poland using high-frequency marker haplotypes. The dataset consisted of phenotypic, genotypic, and pedigree data of 1216 Polish Holstein-Friesian bulls. The genotypic data consisted of 54,000 single-nucleotide polymorphisms (SNPs). The data were divided into two subsets: a test dataset (n = 1064) and a validation dataset (n = 152). Genotypic data were selected using three criteria: the percentage of missing genotypes, minor allele frequency, and linkage disequilibrium. The purpose of the data selection was to identify blocks of SNPs that were then used for the construction of haplotypes. Only haplotypes with a frequency higher than 25% were selected. DGV was predicted using four variants of a linear model with random haplotype effects and deregressed breeding values as the response variables. The accuracy of genomic prediction was checked by comparing DGVs with estimated breeding values (EBVs) using two methods: Pearson’s correlations and the regression of EBV on DGV. The use of high-frequency haplotypes showed a tendency to underestimate DGVs. None of the models tested was clearly superior with regard to the traits studied. DGVs of production and conformation traits as well as somatic cell score (medium or high heritability traits) were more accurate than those estimated for fertility traits (low heritability traits).
Highlights
The genomic selection introduced by Meuwissen et al (2001) has received much attention in animal breeding, because it provides predictions of the breeding values at a young age of animals with higher accuracy than breeding values based on parent average (Hess et al 2017; Van Raden 2008)
DGVs of production and conformation traits as well as somatic cell score were more accurate than those estimated for fertility traits
Haplotypes were constructed on the basis of the blocks selected—those selected from singlenucleotide polymorphisms (SNPs) fulfilling the criteria of minor allele frequency (MAF) > 0.01 and r2 ≥ 0.8 were considered the best set for haplotype construction
Summary
The genomic selection introduced by Meuwissen et al (2001) has received much attention in animal breeding, because it provides predictions of the breeding values at a young age of animals with higher accuracy than breeding values based on parent average (Hess et al 2017; Van Raden 2008). The potential benefits of using genomic selection were outlined by Schaeffer (2006). He showed that the genetic progress of a selected population of Canadian Holstein cattle would be doubled compared to the selection based on offspring phenotypes. He stated that the use of genomic selection would reduce. Building haplotypes based on linkage disequilibrium reduces the number of variables without the loss of information (Cuyabano et al 2014)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
