Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows

Christos Dadousis; Michela Ablondi; Claudio Cipolat-Gotet; Jan-Thijs van Kaam; Raffaella Finocchiaro; Maurizio Marusi; Martino Cassandro; Alberto Sabbioni; Andrea Summer

doi:10.3389/fvets.2023.1142476

Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows

Front Vet Sci. 2023 Apr 28:10:1142476. doi: 10.3389/fvets.2023.1142476. eCollection 2023.

Authors

Christos Dadousis¹, Michela Ablondi¹, Claudio Cipolat-Gotet¹, Jan-Thijs van Kaam², Raffaella Finocchiaro², Maurizio Marusi², Martino Cassandro^{2

3}, Alberto Sabbioni¹, Andrea Summer¹

Affiliations

¹ Department of Veterinary Science, University of Parma, Parma, Italy.
² Associazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana (ANAFIBJ), Cremona, Italy.
³ Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Legnaro, Italy.

Abstract

The objective of this study was to evaluate the effect of imputation of single nucleotide polymorphisms (SNP) on the estimation of genomic inbreeding coefficients. Imputed genotypes of 68,127 Italian Holstein dairy cows were analyzed. Cows were initially genotyped with two high density (HD) SNP panels, namely the Illumina Infinium BovineHD BeadChip (678 cows; 777,962 SNP) and the Genomic Profiler HD-150K (641 cows; 139,914 SNP), and four medium density (MD): GeneSeek Genomic Profiler 3 (10,679 cows; 26,151 SNP), GeneSeek Genomic Profiler 4 (33,394 cows; 30,113 SNP), GeneSeek MD (12,030 cows; 47,850 SNP) and the Labogena MD (10,705 cows; 41,911 SNP). After imputation, all cows had genomic information on 84,445 SNP. Seven genomic inbreeding estimators were tested: (i) four PLINK v1.9 estimators (F, F_hat1,2,3), (ii) two genomic relationship matrix (grm) estimators [VanRaden's 1^st method, but with observed allele frequencies (F_grm) and VanRaden's 3^rd method that is allelic free and pedigree dependent (F_grm2)], and (iii) a runs of homozygosity (roh) - based estimator (F_roh). Genomic inbreeding coefficients of each SNP panel were compared with genomic inbreeding coefficients derived from the 84,445 imputation SNP. Coefficients of the HD SNP panels were consistent between genotyped-imputed SNP (Pearson correlations ~99%), while variability across SNP panels and estimators was observed in the MD SNP panels, with Labogena MD providing, on average, more consistent estimates. The robustness of Labogena MD, can be partly explained by the fact that 97.85% of the SNP of this panel is included in the 84,445 SNP selected by ANAFIBJ for routine genomic imputations, while this percentage for the other MD SNP panels varied between 55 and 60%. Runs of homozygosity was the most robust estimator. Genomic inbreeding estimates using imputation SNP are influenced by the SNP number of the SNP panel that are included in the imputed SNP, and performance of genomic inbreeding estimators depends on the imputation.

Keywords: dairy cattle; genomics; imputation; inbreeding; single nucleotide polymorphism (SNP).

Grants and funding

This study was supported by the Latteco2 project, sottomisura 10.2 of the PSRNBiodiversity 2020–2023 (MIPAAF. D.M. no. 465907 del 24/09/2021, project unique code J12C21004080005). This research benefits from the High Performance Computing facility of the University of Parma, Italy (HPC.unipr.it).