title: Cow genotyping strategies for genomic selection in a small dairy cattle population.
abstract: This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can improve the accuracy of genomic EBV. The Guernsey breed is a small dairy cattle breed with approximately 14,000 recorded individuals worldwide. Predictions of phenotypes of milk yield, fat yield, protein yield, and calving interval were made for Guernsey cows from England and Guernsey Island using genomic EBV, with training sets including 197 de-regressed proofs of genotyped bulls, with cows selected from among 1,440 genotyped cows using different genotyping strategies. Accuracies of predictions were tested using 10-fold cross-validation among the cows. Genomic EBV were predicted using 4 different methods: (1) pedigree BLUP, (2) genomic BLUP using only bulls, (3) univariate genomic BLUP using bulls and cows, and (4) bivariate genomic BLUP. Genotyping cows with phenotypes and using their data for the prediction of single nucleotide polymorphism effects increased the correlation between genomic EBV and phenotypes compared with using only bulls by 0.163±0.022 for milk yield, 0.111±0.021 for fat yield, and 0.113±0.018 for protein yield; a decrease of 0.014±0.010 for calving interval from a low base was the only exception. Genetic correlation between phenotypes from bulls and cows were approximately 0.6 for all yield traits and significantly different from 1. Only a very small change occurred in correlation between genomic EBV and phenotypes when using the bivariate model. It was always better to genotype all the cows, but when only half of the cows were genotyped, a divergent selection strategy was better compared with the random or directional selection approach. Divergent selection of 30% of the cows remained superior for the yield traits in 8 of 10 folds.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom. Electronic address: janez.jenko@roslin.ed.ac.uk.
authors.forename: J
authors.initials: J
authors.lastname: Jenko
authors.affiliation: Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD 20705.
authors.forename: G R
authors.initials: GR
authors.lastname: Wiggans
authors.affiliation: Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD 20705.
authors.forename: T A
authors.initials: TA
authors.lastname: Cooper
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
authors.forename: S A E
authors.initials: SAE
authors.lastname: Eaglen
authors.affiliation: World Guernsey Cattle Federation, The Hollyhocks, 10 Clos des Goddards, Rue des Goddards, Castel GY5 7JD, Guernsey.
authors.forename: W G de L
authors.initials: WGL
authors.lastname: Luff
authors.affiliation: English Guernsey Cattle Society, 12 Southgate Street, Launceston, Cornwall PL15 9DP, United Kingdom.
authors.forename: M
authors.initials: M
authors.lastname: Bichard
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
authors.forename: R
authors.initials: R
authors.lastname: Pong-Wong
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
authors.forename: J A
authors.initials: JA
authors.lastname: Woolliams
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D005260:Female; D016678:Genome; D023281:Genomics; D005838:Genotype; D008297:Male; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Guernsey; cow genotyping strategies; genomic selection; genotyping cows