Optimising multistage dairy cattle breeding schemes including genomic selection using decorrelated or optimum selection indices

Abstract

Background: The prediction of the outcomes from multistage breeding schemes is especially important for the introduction of genomic selection in dairy cattle. Decorrelated selection indices can be used for the optimisation of such breeding schemes. However, they decrease the accuracy of estimated breeding values and, therefore, the genetic gain to an unforeseeable extent and have not been applied to breeding schemes with different generation intervals and selection intensities in each selection path.

Methods: A grid search was applied in order to identify optimum breeding plans to maximise the genetic gain per year in a multistage, multipath dairy cattle breeding program. In this program, different values of the accuracy of estimated genomic breeding values and of their costs per individual were applied, whereby the total breeding costs were restricted. Both decorrelated indices and optimum selection indices were used together with fast multidimensional integration algorithms to produce results.

Results: In comparison to optimum indices, the genetic gain with decorrelated indices was up to 40% less and the proportion of individuals undergoing genomic selection was different. Additionally, the interaction between selection paths was counter-intuitive and difficult to interpret. Independent of using decorrelated or optimum selection indices, genomic selection replaced traditional progeny testing when maximising the genetic gain per year, as long as the accuracy of estimated genomic breeding values was ≥ 0.45. Overall breeding costs were mainly generated in the path "dam-sire". Selecting males was still the main source of genetic gain per year.

Conclusion: Decorrelated selection indices should not be used because of misleading results and the availability of accurate and fast algorithms for exact multidimensional integration. Genomic selection is the method of choice when maximising the genetic gain per year but genotyping females may not allow for a reduction in overall breeding costs. Furthermore, the economic justification of genotyping females remains questionable.

Figure 1

Standard pedigree used to derive breeding values in all selection paths.

Figure 2

Comparison of results when decorrelated (DSI) or optimum selection indices (OSI) were applied. Figure 2(a) shows the genetic gain per year from applying DSI as a proportion of the one from applying OSI. Figure 2(b) shows the genetic gain per generation of different selection paths of breeding schemes that maximise the genetic gain per year given an accuracy and cost of estimated genomic breeding values of 0.75 and of 150 €, respectively, when the proportion of genotyped males is varied along the x-axis and all other parameters were chosen such that the genetic gain per year was maximised; paths "sire-sire" (Δ) "sire-dam" (□) and "dam-sire" (+) calculated with optimum indices, and of the paths "sire-sire" (∇), "sire-dam" (◊) and "dam-sire" (x) calculated with decorrelated indices

Figure 3

Characteristics of breeding schemes that maximise the genetic gain per year when optimum selection indices were used. 3(a) Proportion of genotyped initial selection candidates in the sire-dam path 3(b) Proportion of progeny tested initial selection candidates in the sire-dam path 3(c) Proportion of genotyped initial selection candidates in the dam-sire path 3(d) Genetic gain per year 3(e) Total breeding cost as proportion of the maximum cost 3(f) Breeding cost of the dam-sire path as proportion of total breeding cost