Abstract
BackgroundThe 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.MethodsA 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.ResultsIn 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.ConclusionDecorrelated 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.
Highlights
Genomic selection (GS) offers breeders the opportunity to reduce costs, decrease the generation interval [1] and possibly avoid inbreeding [2]
Comparison of methods to calculate genetic gain Parameters and results of the breeding schemes that maximise Δ Ga and fulfill the cost constraint were compared between optimum selection indices (OSI) and DSL Table 2 summarises the frequency of certain selection strategies of optimum breeding schemes in paths SS, SD and DS as a function of TGEBV and the application of either OSI or DSL For selection in path SD with rQEBV ranging from 0.3 to 0.4, both methods found that combined selection at PED and GS stage or a three-stage selection approach maximised Δ Ga
Results using the optimum index In this study, we found for a given TGEBV of 0.75, a Δ Ga between 0.53 and 0.57 genetic standard deviation, which is higher than found in other published results [1,27]
Summary
Genomic selection (GS) offers breeders the opportunity to reduce costs, decrease the generation interval [1] and possibly avoid inbreeding [2]. GS is based on the prediction of breeding values from individual genotypes (estimated genomic breeding values, GEBV). These genotypes consist of a large number of DNA markers in the form of single nucleotide polymorphisms (SNP), which are in linkage disequilibrium with quantitative trait loci coding for economically important traits. Schaeffer [1] summarised the potential effects of GS on dairy cattle breeding schemes assuming an rGEBV of 0.75 and a cost for GS per genotyped individual (CQEBV) of 500 Canadian Dollars in a one-stage selection approach. Decorrelated selection indices can be used for the optimisation of such breeding schemes They decrease the accuracy of estimated breeding values and, 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
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
