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| Gredler, B.; Sargolzaei, M.; Bapst, B.; Bieber, A.; Simianer, H.; Seefried, F.R.. |
| Imputation of genotypes can be used to reduce the implementation costs of genomic selection. In this study, we evaluated the accuracy of genotype imputation from Illumina 54k to Illumina High Density (HD) in Brown Swiss cattle. Genotype data comprised 6,106 54k and 880 HD genotyped bulls and cows of Brown Swiss and Original Braunvieh cattle. Genotype data was checked for parentage conflicts and SNP were excluded if MAF was below 0.5% and SNP call rate was lower than 90%. The final data set included 39,004 SNP for the 54k and 627,306 SNP for the HD chip. HD genotypes of animals born between 2004 and 2008 (n=365) were masked to mimic animals genotyped with the 54k chip. Methods used for imputation were FImpute and Findhap V2. Both programs use pedigree... |
| Tipo: Conference paper, poster, etc. |
Palavras-chave: Breeding and genetics. |
| Ano: 2013 |
URL: http://orgprints.org/36412/1/Gredler-etal-2013_Plant_Animal_Genome_XXI_Congress_SanDiego_USA.pdf |
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| Kramer, M.; Erbe, M.; Seefried, F.R.; Gredler, B.; Bapst, B.; Bieber, A.; Simianer, H.. |
| In this study, direct genomic values for the functional traits general temperament, milking temperament, aggressiveness, rank order in herd, milking speed, udder depth, position of labia, and days to first heat in Brown Swiss dairy cattle were estimated based on ∼777,000 (777k) single nucleotide polymorphism (SNP) information from 1,126 animals. Accuracy of direct genomic values was assessed by a 5-fold cross-validation with 10 replicates. Correlations between deregressed proofs and direct genomic values were 0.63 for general temperament, 0.73 for milking temperament, 0.69 for aggressiveness, 0.65 for rank order in herd, 0.69 for milking speed, 0.71 for udder depth, 0.66 for position of labia, and 0.74 for days to first heat. Using the information of... |
| Tipo: Journal paper |
Palavras-chave: Beef cattle; Breeding and genetics. |
| Ano: 2014 |
URL: http://orgprints.org/25080/1/Kramer_2014_Accuracy%20of%20direct%20genomic%20values.pdf |
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| Bapst, B.; Baes, C.; Seefried, F.R.; Bieber, A.; Simianer, H.; Gredler, B.. |
| The effect of including 1,236 cows in the current reference population of Swiss Brown Swiss cattle on the accuracy of genomic breeding values was studied. The accuracy of genomic predictions based on reference populations consisting of bulls only and bulls and cows was compared. The gain in accuracy was very small or not existing at all. Reasons could be that the number of cows was too small for a reference population consisting of 4,085 bulls and that the cows and bulls were too closely related. Nevertheless, genotyping cows and subsequent inclusion in the reference population should be accelerated. |
| Tipo: Conference paper, poster, etc. |
Palavras-chave: Breeding and genetics. |
| Ano: 2013 |
URL: http://orgprints.org/36411/1/Bapst-etal-2013-Interbull-Bulletin-No47-p187-191.pdf |
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| Frischknecht, M.; Meuwissen, T.H.E.; Bapst, B.; Seefried, F.R.; Flury, C.; Garrick, D.; Signer-Hasler, H.; Stricker, C.; Consortium, Intergenomics; Bieber, Anna; Fries, R.; Russ, I.; Sölkner, J.; Bagnato, A.; Gredler-Grandl, B.. |
| The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in... |
| Tipo: Journal paper |
Palavras-chave: Dairy cattle; Breeding and genetics. |
| Ano: 2018 |
URL: http://orgprints.org/35104/1/Frischknecht-etal-2018-JDairySci-Vol101-Issue2-p1292-1296.pdf |
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