Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds.
SNP panel
breed assignment
classification
informative SNPs
local breeds
partial least squares
Journal
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
ISSN: 1439-0388
Titre abrégé: J Anim Breed Genet
Pays: Germany
ID NLM: 100955807
Informations de publication
Date de publication:
Jan 2022
Jan 2022
Historique:
revised:
06
08
2021
received:
11
03
2021
accepted:
08
08
2021
pubmed:
25
8
2021
medline:
17
12
2021
entrez:
24
8
2021
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
40-61Subventions
Organisme : Service Public de Wallonie
Organisme : Terra Teaching and Research Centre
Organisme : Administration of Technical Agricultural Services
Organisme : INTERREG V France-Wallonie-Vlaanderen
ID : 2.3.284
Organisme : Fonds De La Recherche Scientifique - FNRS
ID : T.0095.19
Organisme : Fonds De La Recherche Scientifique - FNRS
ID : J.0174.18
Informations de copyright
© 2021 Wiley-VCH GmbH.
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