Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

Abstract

Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed‐informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross‐validation, 14 models had a global cross‐validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares‐discriminant analysis (PLS‐DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS‐DA method when selecting breed‐informative SNPs.

203. Is it possible to differentiate meat products of a local breed from those of its sister breed based on genotypes?

“…The PCA was based on a total of 17,667 SNPs as in a previous study (Wilmot et al, 2022) and on the first dataset. Missing values per individual were imputed following a procedure of the missMDA v1.18 R package (Josse and Husson, 2012), related to PCA, and described in Wilmot et al (2022). The FactomineR v.2.4 R package (Lê et al, 2008) was used to perform the PCA on the matrix of correlations.…”

The pattern of linkage disequilibrium in Dual‐Purpose Belgian Blue cattle

“…Individuals were genotyped using the BovineSNP50 Beadchip v1 to 3 and EuroG MD (SI) v9 (Illumina, San Diego, CA, USA). A total of 28,427 SNPs, common between all the four chips, passed the following filters on no non‐mapped SNPs, no SNPs located on sexual chromosomes, no triallelic SNPs, minimum GenCall Score of 0.15 and minimum GenTrain Score of 0.55 (Wilmot et al., 2021). The difference between observed heterozygosity and that expected under Hardy–Weinberg equilibrium was estimated, separately for each SNP in each breed, and if the difference was greater than 0.15, the SNP was excluded (Wiggans et al., 2009).…”

Genome‐wide association for milk urea concentration in Dual‐Purpose Belgian Blue cows

“…A minimum GenCall Score of 0.15 and minimum GenTrain Score of 0.55 were used to keep SNPs. (Wilmot et al, 2022). SNP with Mendelian conflicts and minor allele frequency (MAF) lower than 5% were excluded.…”