title: Including nonadditive genetic effects in mating programs to maximize dairy farm profitability.
abstract: We compared the outcome of mating programs based on different evaluation models that included nonadditive genetic effects (dominance and heterozygosity) in addition to additive effects. The additive and dominance marker effects and the values of regression on average heterozygosity were estimated using 632,003 single nucleotide polymorphisms from 7,902 and 7,510 Holstein cows with calving interval and production (milk, fat, and protein yields) records, respectively. Expected progeny values were computed based on the estimated genetic effects and genotype probabilities of hypothetical progeny from matings between the available genotyped cows and the top 50 young genomic bulls. An index combining the traits based on their economic values was developed and used to evaluate the performance of different mating scenarios in terms of dollar profit. We observed that mating programs with nonadditive genetic effects performed better than a model with only additive effects. Mating programs with dominance and heterozygosity effects increased milk, fat, and protein yields by up to 38, 1.57, and 1.21 kg, respectively. The inclusion of dominance and heterozygosity effects decreased calving interval by up to 0.70 d compared with random mating. The average reduction in progeny inbreeding by the inclusion of nonadditive genetic effects in matings compared with random mating was between 0.25 to 1.57 and 0.64 to 1.57 percentage points for calving interval and production traits, respectively. The reduction in inbreeding was accompanied by an average of A$8.42 (Australian dollars) more profit per mating for a model with additive, dominance, and heterozygosity effects compared with random mating. Mate allocations that benefit from nonadditive genetic effects can improve progeny performance only in the generation where it is being implemented, and the gain from specific combining abilities cannot be accumulated over generations. Continuous updating of genomic predictions and mate allocation programs are required to benefit from nonadditive genetic effects in the long term.
authors.affiliation: Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia. Electronic address: haliloo@une.edu.au.
authors.forename: H
authors.initials: H
authors.lastname: Aliloo
authors.affiliation: Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia.
authors.forename: J E
authors.initials: JE
authors.lastname: Pryce
authors.affiliation: Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; Department of Animal Breeding, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra La Coruña, 28040 Madrid, Spain.
authors.forename: O
authors.initials: O
authors.lastname: González-Recio
authors.affiliation: Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia.
authors.forename: B G
authors.initials: BG
authors.lastname: Cocks
authors.affiliation: Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; Faculty of Veterinary and Agricultural Sciences, Department of Agriculture and Food Systems, The University of Melbourne, Parkville, VIC 3010, Australia.
authors.forename: M E
authors.initials: ME
authors.lastname: Goddard
authors.affiliation: Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia; Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia.
authors.forename: B J
authors.initials: BJ
authors.lastname: Hayes
mesh_terms: D000818:Animals; D001315:Australia; D001947:Breeding; D002417:Cattle; D000072480:Farms; D005260:Female; D007178:Inbreeding; D008297:Male; D008892:Milk / Q000378:metabolism; D008957:Models, Genetic
keywords: inbreeding; nonadditive genetic effect; planned mating; specific combining ability