Genomic selection improves the possibility of applying multiple breeding programs in different environments

ABSTRACT

One joint breeding program (BP) for different dairy cattle environments can be advantageous for genetic gain depending on the genetic correlation between environments (r_g). The break-even correlation (r_b) refers to the specific r_g where genetic gain with 1 joint BP is equal to the genetic gain of 2 environment-specific BP. One joint BP has the highest genetic gain if r_g is higher than r_b, whereas 2 environment-specific BP have higher genetic gain if r_g is lower than r_b. Genetic gain in this context is evaluated from a breeding company's perspective that aims to improve genetic gain in both environments. With the implementation of genomic selection, 2 types of collaboration can be identified: exchanging breeding animals and exchanging genomic information. The aim of this study was to study genetic gain in multiple environments with different breeding strategies with genomic selection. The specific aims were (1) to find r_b when applying genomic selection; (2) to assess how much genetic gain is lost when applying a suboptimal breeding strategy; (3) to study the effect of the reliability of direct genomic values, number of genotyped animals, and environments of different size on r_b and genetic gain; and (4) to find r_b from each environment's point of view. Three breeding strategies were simulated: 1 joint BP for both environments, 2 environment-specific BP with selection of bulls across environments, and 2 environment-specific BP with selection of bulls within environments. The r_b was 0.65 and not different from r_b with progeny-testing breeding programs when compared at the same selection intensity. The maximum loss in genetic gain in a suboptimal breeding strategy was 24%. A higher direct genomic value reliability and an increased number of genotyped selection candidates increased genetic gain, and the effect on r_b was not large. A different size in 2 environments decreased r_b by, at most, 0.10 points. From a large environment's point of view, 1 joint BP was the optimal breeding strategy in most scenarios. From a small environment's point of view, 1 joint BP was only the optimal breeding strategy at high r_g. When the exchange of breeding animals between environments was restricted, genetic gain could still increase in each environment. This was due to the exchange of genomic information between environments, even when r_g between environments were as low as 0.4. Thus, genomic selection improves the possibility of applying environment-specific BP.