title: Adding cows to the reference population makes a small dairy population competitive.
abstract: Small dairy breeds are challenged by low reliabilities of genomic prediction. Therefore, we evaluated the effect of including cows in the reference population for small dairy cattle populations with a limited number of sires in the reference population. Using detailed simulations, 2 types of scenarios for maintaining and updating the reference population over a period of 15yr were investigated: a turbo scheme exclusively using genotyped young bulls and a hybrid scheme with mixed use of genotyped young bulls and progeny-tested bulls. Two types of modifications were investigated: (1) number of progeny-tested bulls per year was tested at 6 levels: 15, 40, 60, 100, 250, and 500; and (2) each year, 2,000 first-lactation cows were randomly selected from the cow population for genotyping or, alternatively, an additional 2,000 first-lactation cows were randomly selected and typed in the first 2yr. The effects were evaluated in the 2 main breeding schemes. The breeding schemes were chosen to mimic options for the Danish Jersey cattle population. Evaluation criteria were annual monetary genetic gain, rate of inbreeding, reliability of genomic predictions, and variance of response. Inclusion of cows in the reference population increased monetary genetic gain and decreased the rate of inbreeding. The increase in genetic gain was larger for the turbo schemes with shorter generation intervals. The variance of response was generally higher in turbo schemes than in schemes using progeny-tested bulls. However, the risk was reduced by adding cows to the reference population. The annual genetic gain and the reliability of genomic predictions were slightly higher with more cows in the reference population. Inclusion of cows in the reference population is a rapid way to increase reliabilities of genomic predictions and hence increase genetic gain in a small population. An economic evaluation shows that genotyping of cows is a profitable investment.
authors.affiliation: VikingGenetics, DK 8860, Assentoft, Denmark; Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, DK-8830, Tjele, Denmark. Electronic address: jotho@vikinggenetics.com.
authors.forename: J R
authors.initials: JR
authors.lastname: Thomasen
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, DK-8830, Tjele, Denmark.
authors.forename: A C
authors.initials: AC
authors.lastname: Sørensen
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, DK-8830, Tjele, Denmark.
authors.forename: M S
authors.initials: MS
authors.lastname: Lund
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, DK-8830, Tjele, Denmark.
authors.forename: B
authors.initials: B
authors.lastname: Guldbrandtsen
mesh_terms: D000818:Animals; D001947:Breeding / Q000191:economics / Q000379:methods*; D002417:Cattle / Q000235:genetics* / Q000254:growth & development; D003612:Dairying / Q000191:economics / Q000379:methods*; D003718:Denmark; D005260:Female; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008297:Male; D008957:Models, Genetic; D011156:Population Density; D015203:Reproducibility of Results; D012641:Selection, Genetic
keywords: genomic breeding plan; genomic selection; genotyped cow