Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows
ABSTRACT: The objective of this study was to estimate inbreeding coefficients in Holstein dairy cattle using imputed SNPs data. A data set of 95,540 Italian Holstein dairy cows from the routine genomic evaluations of the Italian National Association of Holstein, Brown, and Jersey Breeders were analy...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-07-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030222002685 |
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| author | Christos Dadousis Michela Ablondi Claudio Cipolat-Gotet Jan-Thijs van Kaam Maurizio Marusi Martino Cassandro Alberto Sabbioni Andrea Summer |
| author_facet | Christos Dadousis Michela Ablondi Claudio Cipolat-Gotet Jan-Thijs van Kaam Maurizio Marusi Martino Cassandro Alberto Sabbioni Andrea Summer |
| author_sort | Christos Dadousis |
| collection | DOAJ |
| description | ABSTRACT: The objective of this study was to estimate inbreeding coefficients in Holstein dairy cattle using imputed SNPs data. A data set of 95,540 Italian Holstein dairy cows from the routine genomic evaluations of the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed, with 84,445 imputed SNP. Ten widely used genomic inbreeding estimators were tested, including 4 PLINK v1.9 estimators (F, FHAT1, FHAT2, FHAT3), 3 genomic relationship matrix (GRM)-based methods [VanRaden's first method with observed allele frequencies (FGRM) or with fixed frequencies at 0.5 (FGRM05), VanRaden's third method, allelic frequency free and pedigree regressed (FGRM2)], runs of homozygosity (ROH)-based estimators in a complete (FROH) and simplified version (FROH2), and proportion of homozygous SNP (FPH). Pairwise comparisons among them were made, including the comparison with traditional pedigree-based inbreeding coefficients (FPED). Our results showed variability among the genomic inbreeding estimators. Coefficients of FGRM and FHAT3 were >1, meaning that more variability has been lost than the variability that existed in the base population. Regarding the remaining ones, FGRM05, FROH, FROH2, and FPH provided coefficients within the [0,1] space and are considered comparable to FPED. Not comparable to FPED, yet with an interpretable value, can be considered the coefficients of F, FHAT2, and FGRM2. Estimators based on ROH had the highest correlation with pedigree-based coefficients (0.59–0.66), among all estimators tested. In this study, Spearman correlations were shown to possibly provide a clearer estimation of the strength of the relationship between estimators. We hypothesize that imputation might cause extreme genomic inbreeding values that deserves further investigation. |
| first_indexed | 2024-12-12T15:02:40Z |
| format | Article |
| id | doaj.art-cd3807420ce94e84b5f7ad609cf2fb9f |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-12-12T15:02:40Z |
| publishDate | 2022-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dairy Science |
| spelling | doaj.art-cd3807420ce94e84b5f7ad609cf2fb9f2022-12-22T00:20:46ZengElsevierJournal of Dairy Science0022-03022022-07-01105759265945Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cowsChristos Dadousis0Michela Ablondi1Claudio Cipolat-Gotet2Jan-Thijs van Kaam3Maurizio Marusi4Martino Cassandro5Alberto Sabbioni6Andrea Summer7Department of Veterinary Science, University of Parma, 43126 Parma, Italy; Corresponding authorDepartment of Veterinary Science, University of Parma, 43126 Parma, ItalyDepartment of Veterinary Science, University of Parma, 43126 Parma, ItalyAssociazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, ItalyAssociazione Nazionale Allevatori della Razza Frisona Bruna e Jersey Italiana, (ANAFIBJ), 26100 Cremona, ItalyAssociazione 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), ItalyDepartment of Veterinary Science, University of Parma, 43126 Parma, ItalyDepartment of Veterinary Science, University of Parma, 43126 Parma, ItalyABSTRACT: The objective of this study was to estimate inbreeding coefficients in Holstein dairy cattle using imputed SNPs data. A data set of 95,540 Italian Holstein dairy cows from the routine genomic evaluations of the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed, with 84,445 imputed SNP. Ten widely used genomic inbreeding estimators were tested, including 4 PLINK v1.9 estimators (F, FHAT1, FHAT2, FHAT3), 3 genomic relationship matrix (GRM)-based methods [VanRaden's first method with observed allele frequencies (FGRM) or with fixed frequencies at 0.5 (FGRM05), VanRaden's third method, allelic frequency free and pedigree regressed (FGRM2)], runs of homozygosity (ROH)-based estimators in a complete (FROH) and simplified version (FROH2), and proportion of homozygous SNP (FPH). Pairwise comparisons among them were made, including the comparison with traditional pedigree-based inbreeding coefficients (FPED). Our results showed variability among the genomic inbreeding estimators. Coefficients of FGRM and FHAT3 were >1, meaning that more variability has been lost than the variability that existed in the base population. Regarding the remaining ones, FGRM05, FROH, FROH2, and FPH provided coefficients within the [0,1] space and are considered comparable to FPED. Not comparable to FPED, yet with an interpretable value, can be considered the coefficients of F, FHAT2, and FGRM2. Estimators based on ROH had the highest correlation with pedigree-based coefficients (0.59–0.66), among all estimators tested. In this study, Spearman correlations were shown to possibly provide a clearer estimation of the strength of the relationship between estimators. We hypothesize that imputation might cause extreme genomic inbreeding values that deserves further investigation.http://www.sciencedirect.com/science/article/pii/S0022030222002685inbreedingsingle nucleotide polymorphismimputationdairy cattle |
| spellingShingle | Christos Dadousis Michela Ablondi Claudio Cipolat-Gotet Jan-Thijs van Kaam Maurizio Marusi Martino Cassandro Alberto Sabbioni Andrea Summer Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows Journal of Dairy Science inbreeding single nucleotide polymorphism imputation dairy cattle |
| title | Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows |
| title_full | Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows |
| title_fullStr | Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows |
| title_full_unstemmed | Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows |
| title_short | Genomic inbreeding coefficients using imputed genotypes: Assessing different estimators in Holstein-Friesian dairy cows |
| title_sort | genomic inbreeding coefficients using imputed genotypes assessing different estimators in holstein friesian dairy cows |
| topic | inbreeding single nucleotide polymorphism imputation dairy cattle |
| url | http://www.sciencedirect.com/science/article/pii/S0022030222002685 |
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