breed assignment; classification; informative SNPs; local breeds; partial least squares; SNP panel
Abstract :
[en] 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.
Disciplines :
Animal production & animal husbandry
Author, co-author :
Wilmot, Hélène ; Université de Liège - ULiège > Département GxABT > Ingénierie des productions animales et nutrition
Bormann, Jeanne; Gouvernement du Grand Duché de Luxembourg Ministère de l'Agriculture, de la Viticulture et du Développement rural > Administration des services techniques de l'agriculture > Service de la production animale
Soyeurt, Hélène ; Université de Liège - ULiège > Département GxABT > Modélisation et développement
Hubin, Xavier; awé groupe > elevéo > R&D
Glorieux, Géry; awé groupe > elevéo > Service bovins viande
Mayeres, Patrick; awé groupe > elevéo
Bertozzi, Carlo; awé groupe > elevéo
Gengler, Nicolas ; Université de Liège - ULiège > Département GxABT > Ingénierie des productions animales et nutrition
Language :
English
Title :
Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds
Publication date :
January 2022
Journal title :
Journal of Animal Breeding and Genetics
ISSN :
0931-2668
eISSN :
1439-0388
Publisher :
Wiley, Oxford, United Kingdom
Volume :
139
Issue :
1
Pages :
40-61
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
Commentary :
This is the accepted version of the following article: Wilmot H, Bormann J, Soyeurt H, Hubin X, Glorieux G, Mayeres P, Bertozzi C, Gengler N. Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds. J Anim Breed Genet. 2022 Jan;139(1):40-61. doi: 10.1111/jbg.12643. Epub 2021 Aug 24. PMID: 34427366., which has been published in final form at https://onlinelibrary.wiley.com/doi/full/10.1111/jbg.12643
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