Breeding and Genetics: Genomic Selection Methods II

Computer mating programs have helped breeders minimize pedigree inbreeding and avoid recessive defects by mating animals with parents that have fewer common ancestors. With genomic selection, breed associations, AI organizations, and on-farm software providers could use new programs to minimize genomic inbreeding by comparing genotypes of potential mates. Relationships could be computed between (1) only requested males and females via a web query, or (2) all genotyped females with only the marketed males (e.g., >200,000 females and >1,500 bulls), because (3) relationships between all >300,000 genotyped animals are difficult to store and transfer. To compare mating strategies, 50 marketed bulls in each of breed (Jersey and Holstein) were selected for top genomic Lifetime Net Merit (LNM), top traditional LNM, or randomly selected. The 500 youngest genotyped females in the largest herd were assigned mates of the same breed with limits of 10 females per bull and 1 bull per cow (for Brown Swiss, only 79 females and 8 bulls were included). Linear programming, a simpler method that assigned least related mates sequentially, and random mating were compared. For each method, calf value was the average of parents’ genomic LNM plus the inbreeding loss times average of parents’ expected future inbreeding, minus inbreeding loss time parents’ genomic or pedigree relationship. A value of $23.11/1% was assumed for inbreeding loss for all mating methods. Compared with random mating, assigning mates using pedigree inbreeding gave only about 60% of the advantage of using genomic inbreeding for Holsteins, and the simpler mating strategy gave about 90% of the linear programming advantage. The economic value of a mating strategy that uses linear programming and genomic instead of pedigree inbreeding is already >$2 million per year for Holsteins and will grow as more females are genotyped. Eventually, dominance effects could also be included in mating programs to estimate inbreeding losses more precisely. Software to estimate dominance variance and to estimate the dominance effect for each SNP could allow mating plans to include both dominance effects and genomic inbreeding.