Optimization of a genomic breeding program for a moderately sized dairy cattle population

Although it is now standard practice to genotype thousands of female calves, genotyping of bull calves is still limited to progeny of elite cows. In addition to genotyping costs, increasing the pool of candidate sires requires purchase, isolation and identification of calves until selection decisions are made. We economically optimized via simulation a genomic breeding program for a population of ~120,000 milk-recorded cows, corresponding to the Israeli Holstein population. All 30,000 heifers and 60,000 older cows of parities 2-4 were potential bull dams. Animals were assumed to have genetic evaluations for a trait with heritability of 0.25 derived by an animal model evaluation of the population. A pseudo phenotype was generated, consisting of the animal's genetic value plus a residual with variance set to obtain the assumed reliability for each group of animals. Genetic values of founder heifers were simulated by sampling from a normal distribution with a mean of zero, and a variance of unity. Genetic values of older cows were generated with the same variance, but with means decreasing by 0.2 for each additional parity, to reflect the assumed genetic gain per year. Reliabilities increased with cow age. Forty founder sires were simulated in a similar manner assuming reliabilities of 0.9, and a mean genetic value of zero. From 4 to 20 bulls and from 200 to 27,000 cows with the highest pseudo phenotypes were selected as candidate bull parents. For all progeny of the founder animals, genetic values were simulated as the mean of the parental values plus a Mendelian sampling effect with a variance of 0.5. A probability of 0.3 for a healthy bull calf per mating, and a genomic reliability of 0.43 were assumed. The 40 bull calves with the highest genomic evaluations were selected for general service for 1 yr. Cost included genotyping of candidate bulls and their dames, purchase of the calves from the farmers and identification. Costs of raising culled calves were recovered by resale for beef. Annual costs dependent on the number of candidate bulls were estimated as: $10,650 + $300·candidate bulls. Annual profit per cow per genetic SD was $106. Economic optimum with a discount rate of 5% and a profit horizon of 15 yr was obtained with 1650 to 1850 candidate bulls. Annual response to selection ranged from 0.4 to 0.35 genetic SD for 4 to 20 bull sires.