Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle
ABSTRACT: This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IAm) and by individual (IAi) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate IA from a low- (7K) to a medium-density (50K) SNP chip. Crossbred animals, as well as their sires...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-01-01
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| Series: | Journal of Dairy Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0022030223004873 |
| _version_ | 1797356114891767808 |
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| author | Vanille Déru Francesco Tiezzi Paul M. VanRaden Emmanuel A. Lozada-Soto Sajjad Toghiani Christian Maltecca |
| author_facet | Vanille Déru Francesco Tiezzi Paul M. VanRaden Emmanuel A. Lozada-Soto Sajjad Toghiani Christian Maltecca |
| author_sort | Vanille Déru |
| collection | DOAJ |
| description | ABSTRACT: This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IAm) and by individual (IAi) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate IA from a low- (7K) to a medium-density (50K) SNP chip. Crossbred animals, as well as their sires (53), dams (77), and maternal grandsires (63), were all genotyped with a 78K SNP chip. Seven different scenarios of reference populations were tested, in which some scenarios used different family relationships and others added random unrelated purebred and crossbred individuals to those different family relationship scenarios. The same scenarios were tested on Holstein and Jersey purebred animals to compare these outcomes against those attained in crossbred animals. The genotype imputation was performed with findhap (version 4) software (VanRaden, 2015). There were no significant differences in IA results depending on whether the sire of imputed individuals was Holstein and the dam was Jersey, or vice versa. The IA increased significantly with the addition of related individuals in the reference population, from 86.70 ± 0.06% when only sires or dams were included in the reference population to 90.09 ± 0.06% when sire (S), dam (D), and maternal grandsire genomic data were combined in the reference population. In all scenarios including related individuals in the reference population, IAm and IAi were significantly superior in purebred Jersey and Holstein animals than in crossbreds, ranging from 90.75 ± 0.06 to 94.02 ± 0.06%, and from 90.88 ± 0.11 to 94.04 ± 0.10%, respectively. Additionally, a scenario called SPB+DLD(where PB indicates purebread and LD indicates low density), similar to the genomic evaluations performed on US crossbred dairy, was tested. In this scenario, the information from the 5 evaluated breeds (Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey) genotyped with a 50K SNP chip and genomic information from the dams genotyped with a 7K SNP chip were combined in the reference population, and the IAm and IAi were 80.87 ± 0.06% and 80.85 ± 0.08%, respectively. Adding randomly nonrelated genotyped individuals in the reference population reduced IA for both purebred and crossbred cows, except for scenario SPB+DLD, where adding crossbreds to the reference population increased IA values. Our findings demonstrate that IA for US Holstein × Jersey crossbred ranged from 85 to 90%, and emphasize the significance of designing and defining the reference population for improved IA. |
| first_indexed | 2024-03-08T14:22:03Z |
| format | Article |
| id | doaj.art-4013c3d30fbd408987bc36f1e51feed4 |
| institution | Directory Open Access Journal |
| issn | 0022-0302 |
| language | English |
| last_indexed | 2024-03-08T14:22:03Z |
| publishDate | 2024-01-01 |
| publisher | Elsevier |
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| series | Journal of Dairy Science |
| spelling | doaj.art-4013c3d30fbd408987bc36f1e51feed42024-01-14T05:34:43ZengElsevierJournal of Dairy Science0022-03022024-01-011071385398Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattleVanille Déru0Francesco Tiezzi1Paul M. VanRaden2Emmanuel A. Lozada-Soto3Sajjad Toghiani4Christian Maltecca5Department of Animal Science, North Carolina State University, Raleigh, NC 27607; Corresponding authorDepartment of Agriculture, Food, Environment and Forestry, University of Florence, Florence, 50144, ItalyUSDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350Department of Animal Science, North Carolina State University, Raleigh, NC 27607USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350Department of Animal Science, North Carolina State University, Raleigh, NC 27607ABSTRACT: This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IAm) and by individual (IAi) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate IA from a low- (7K) to a medium-density (50K) SNP chip. Crossbred animals, as well as their sires (53), dams (77), and maternal grandsires (63), were all genotyped with a 78K SNP chip. Seven different scenarios of reference populations were tested, in which some scenarios used different family relationships and others added random unrelated purebred and crossbred individuals to those different family relationship scenarios. The same scenarios were tested on Holstein and Jersey purebred animals to compare these outcomes against those attained in crossbred animals. The genotype imputation was performed with findhap (version 4) software (VanRaden, 2015). There were no significant differences in IA results depending on whether the sire of imputed individuals was Holstein and the dam was Jersey, or vice versa. The IA increased significantly with the addition of related individuals in the reference population, from 86.70 ± 0.06% when only sires or dams were included in the reference population to 90.09 ± 0.06% when sire (S), dam (D), and maternal grandsire genomic data were combined in the reference population. In all scenarios including related individuals in the reference population, IAm and IAi were significantly superior in purebred Jersey and Holstein animals than in crossbreds, ranging from 90.75 ± 0.06 to 94.02 ± 0.06%, and from 90.88 ± 0.11 to 94.04 ± 0.10%, respectively. Additionally, a scenario called SPB+DLD(where PB indicates purebread and LD indicates low density), similar to the genomic evaluations performed on US crossbred dairy, was tested. In this scenario, the information from the 5 evaluated breeds (Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey) genotyped with a 50K SNP chip and genomic information from the dams genotyped with a 7K SNP chip were combined in the reference population, and the IAm and IAi were 80.87 ± 0.06% and 80.85 ± 0.08%, respectively. Adding randomly nonrelated genotyped individuals in the reference population reduced IA for both purebred and crossbred cows, except for scenario SPB+DLD, where adding crossbreds to the reference population increased IA values. Our findings demonstrate that IA for US Holstein × Jersey crossbred ranged from 85 to 90%, and emphasize the significance of designing and defining the reference population for improved IA.http://www.sciencedirect.com/science/article/pii/S0022030223004873dairy crossbredimputation accuracySNP chip |
| spellingShingle | Vanille Déru Francesco Tiezzi Paul M. VanRaden Emmanuel A. Lozada-Soto Sajjad Toghiani Christian Maltecca Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle Journal of Dairy Science dairy crossbred imputation accuracy SNP chip |
| title | Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle |
| title_full | Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle |
| title_fullStr | Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle |
| title_full_unstemmed | Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle |
| title_short | Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle |
| title_sort | imputation accuracy from low to medium density snp chips for us crossbred dairy cattle |
| topic | dairy crossbred imputation accuracy SNP chip |
| url | http://www.sciencedirect.com/science/article/pii/S0022030223004873 |
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