Simulation of long-term impact of dairy cattle mating programmes using genomic information at the herd level

Genotyping provides breeders with new information at the single nucleotide polymorphism level that can be used in mating programmes. This study used stochastic simulation to explore the long-term effects of genomic mating allocations combining economic scores and linear programming at the level of commercial herds. The economic scores included genetic level, a favourable monogenic trait (polledness), a recessive genetic defect, and parent relationships. The results showed that compared with only maximising genetic level, including genomic or pedigree relationship in the economic score lowered the rate of pedigree and genomic inbreeding with minimal effect on genetic gain. Including the cost of a recessive genetic defect in the score almost eliminated the risk of expression. We set the start allele frequency of polledness to ∼12%, and the value of polledness varied in the different scenarios (€0, €10, €50, and €100). Including an economic value for polledness of (≥ €50) in the economic score increased the frequency of polled animals by up to 0.037 per generation, without negatively impacting other comparison criteria. The use of genomic relationships was favourable for the rate of genomic inbreeding and performed as well as pedigree relationships concerning the rate of pedigree inbreeding. Limiting the number of females per bull and herd to a maximum of 5% instead of 10% also decreased the rate of inbreeding. The 5% females per bull and herd constraint lowered the variation in carrier frequency for genetic defects, which reduced the risk of mating two carriers of an unknown genetic defect in future generations after the widespread use of carriers in previous generations. However, the 10% females per bull constraint accelerated the increase in the polled allele. Therefore, planning matings with genomic information at the herd level involves important risk management decisions, such as balancing the trade-off between using fewer bulls to increase the polled allele frequency more quickly and using more bulls to reduce the rate of inbreeding and the variation in carrier frequency for genetic defects.