Genomic inbreeding coefficients using imputation genotypes: Assessing the effect of ancestral genotyping in Holstein-Friesian dairy cows.

Autor: Dadousis C; Department of Veterinary Science, University of Parma, 43126 Parma, Italy., Ablondi M; Department of Veterinary Science, University of Parma, 43126 Parma, Italy., Cipolat-Gotet C; Department of Veterinary Science, University of Parma, 43126 Parma, Italy. Electronic address: claudio.cipolatgotet@unipr.it., van Kaam JT; Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy., Finocchiaro R; Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy., Marusi M; Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy., Cassandro M; Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana (ANAFIBJ), 26100 Cremona, Italy; Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro (PD), Italy., Sabbioni A; Department of Veterinary Science, University of Parma, 43126 Parma, Italy., Summer A; Department of Veterinary Science, University of Parma, 43126 Parma, Italy.
Jazyk: angličtina
Zdroj: Journal of dairy science [J Dairy Sci] 2024 Aug; Vol. 107 (8), pp. 5869-5880. Date of Electronic Publication: 2024 Mar 14.
DOI: 10.3168/jds.2024-24042
Abstrakt: The objective of this study was to assess the effect of using or not using the genotypes of the parents of a cow for imputing SNPs on the estimation of genomic inbreeding coefficients of cows. Imputation (i.e., genotyped plus imputed) genotypes from 68,127 Italian Holstein dairy cows registered in the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed. Cows were genotyped with the high-density (HD) Illumina Infinium BovineHD BeadChip and GeneSeek Genomic Profiler HD-150K, and the medium-density (MD) GeneSeek Genomic Profiler 3, GeneSeek Genomic Profiler 4, GeneSeek MD, and the Labogena MD. To assess differences among estimators, genomic inbreeding coefficients were estimated with 4 PLINK v1.9 estimators (F, F hat1 ,F hat2 , andF hat3 ), 2 genomic relationship matrix- (grm) based estimators (F grm and F grm2 , with the latter including also pedigree information), and one estimator of runs of homozygosity (ROH; F ROH ). Assuming that the correct genomic inbreeding coefficients should be those estimated from genotyped SNPs, a comparison of the genomic inbreeding coefficients estimated either with the genotyped SNPs or the SNPs after imputation was made. Information on the presence or absence of genotypic information from sire, dam, and maternal grandsire during the imputation was investigated. Genomic inbreeding coefficients estimated with genotyped SNPs or SNPs after imputation were consistent for F, F hat3 , F grm2 , and F ROH , when at least one of the parents was genotyped. Biased (mainly higher) genomic inbreeding coefficients of imputation SNPs were observed in cows that were genotyped with MD SNP panels whose SNPs were poorly represented in the selected imputation SNP dataset and also did not have their parents genotyped, when compared with what would be expected based on actual genotype data. For cows genotyped with MD the estimators F hat1 , F hat2 , and F grm provided higher genomic inbreeding coefficients of imputation SNPs even with both parents and the maternal grandsire genotyped. Overall, F ROH was the most robust estimator, followed by F and F hat3 . Our findings suggest that SNPs selection, parental genotyping and estimator should be considered for designing imputation strategies in dairy cattle for estimating genomic inbreeding with imputation SNPs. For computing genomic inbreeding coefficients, it is recommendable to have at least one parent genotyped and use an ROH-based estimator.
(© 2024, The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)
Databáze: MEDLINE
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