Investigating the benefits and perils of importing genetic material in small cattle breeding programs via simulation.

Small breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the benefit of import depends on the strength of genotype-by-environment interaction. Import also diminishes the relevance of domestic selection and the use of domestic breeding animals. Introduction of genomic selection has potentially exacerbated this issue, but is also opening the potential for smaller breeding programs. The aim of this paper was to determine when and to what extent small breeding programs benefit from importing genetic material by quantifying the genetic gain as well as the sources of genetic gain. We simulated 2 cattle breeding programs of the same breed that represented a large foreign and a small domestic breeding program. The programs differed in selection parameters of sire selection, and in the initial genetic mean and annual genetic gain. We evaluated a control scenario without the use of foreign sires in the domestic breeding program and 24 scenarios that varied the percentage of domestic dams mated with foreign sires, the genetic correlation between the breeding programs (0.8 or 0.9), and the time of implementing genomic selection in the domestic compared with the foreign breeding program (concurrently or with a 10-yr delay). We compared the scenarios based on the genetic gain and genic standard deviation. Finally, we partitioned breeding values and genetic trends of the scenarios to quantify the contribution of domestic selection and import to the domestic genetic gain. The simulation revealed that when both breeding programs implemented genomic selection simultaneously, the use of foreign sires increased domestic genetic gain only when genetic correlation was 0.9 (10%-18% increase). In contrast, when the domestic breeding program implemented genomic selection with a 10-yr delay, import increased genetic gain at both tested correlations, 0.8 (5%-23% increase) and 0.9 (15%-53% increase). The increase was significant when we mated at least 10% or 25% domestic females with foreign sires and increased with the increasing use of foreign sires, but with a diminishing return. The partitioning analysis revealed that the contribution of import expectedly increased with the increased use of foreign sires. However, the increase did not depend on the genetic correlation and was not proportional to the increase in domestic genetic gain. This represents a peril for small breeding programs because they could be overly relying on import with diminishing returns for the genetic gain, marginal benefit for the genetic variability, and large loss of the domestic germplasm. The benefit and peril of import depends on an interplay of genetic correlation, extent of using foreign sires, and a breeding scheme. It is therefore crucial that small breeding programs assess the possible benefits of import beyond domestic selection. The benefit of import should be weighed against the perils of decreased use of domestic sires and decreased contribution and value of domestic selection.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations.

In this study, we compared genetic gain, genetic variation, and the efficiency of converting variation into gain under different genomic selection scenarios with truncation or optimum contribution selection in a small dairy population by simulation. Breeding programs have to maximize genetic gain but also ensure sustainability by maintaining genetic variation. Numerous studies have shown that genomic selection increases genetic gain. Although genomic selection is a well-established method, small populations still struggle with choosing the most sustainable strategy to adopt this type of selection. We developed a simulator of a dairy population and simulated a model after the Slovenian Brown Swiss population with ∼10,500 cows. We compared different truncation selection scenarios by varying (1) the method of sire selection and their use on cows or bull-dams, and (2) selection intensity and the number of years a sire is in use. Furthermore, we compared different optimum contribution selection scenarios with optimization of sire selection and their usage. We compared scenarios in terms of genetic gain, selection accuracy, generation interval, genetic and genic variance, rate of coancestry, effective population size, and conversion efficiency. The results showed that early use of genomically tested sires increased genetic gain compared with progeny testing, as expected from changes in selection accuracy and generation interval. A faster turnover of sires from year to year and higher intensity increased the genetic gain even further but increased the loss of genetic variation per year. Although maximizing intensity gave the lowest conversion efficiency, faster turnover of sires gave an intermediate conversion efficiency. The largest conversion efficiency was achieved with the simultaneous use of genomically and progeny-tested sires that were used over several years. Compared with truncation selection, optimizing sire selection and their usage increased the conversion efficiency by achieving either comparable genetic gain for a smaller loss of genetic variation or higher genetic gain for a comparable loss of genetic variation. Our results will help breeding organizations implement sustainable genomic selection.