Controlling Inbreeding in Modern Breeding Programs

Modern livestock breeding programs feature accurate breeding value estimation and advanced reproductive technology. Such programs lead to rapid genetic progress, but they also lead to the accumulation of inbreeding via heavy impact of a few selected individuals or families. Inbreeding rates are accelerating in most species, and economic losses due to inbreeding depression in production, growth, health, and fertility are a serious concern. Most research has focused on preservation of rare breeds or maintenance of genetic diversity within closed nucleus breeding schemes. However, the apparently large population size of many livestock breeds is misleading, because inbreeding is primarily a function of selection intensity. Strategies for maintaining variation by restricting relationships between selected animals or by artificially increasing the emphasis on within-family information when estimating breeding values have been suggested, and some approaches seem to provide greater long-term responses than BLUP selection. Corrective mating programs are widely used in some species, and these can be modified to consider selection for economic merit adjusted for inbreeding depression. Selection of parents of AI bulls based on optimal genetic contributions to future generations, which are a function of estimated breeding values and genetic relationships between selected individuals, appears most promising. Rapid implementation of such procedures is necessary to avoid further reductions in effective population size. Missing pedigree information is a problem in practice, and the low net present value of future genetic gains makes it difficult for breeding companies to sacrifice short-term economic gains in favor of long-term diversity issues.