Abstract
BackgroundCommercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is expensive to generate. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. However, both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to explore the cost and imputation accuracy of several alternative genotyping strategies in pedigreed populations.MethodsPedigree and genotype data from a commercial pig population were used. Several alternative genotyping strategies were explored. The strategies differed in the density of genotypes used for the ancestors and the individuals to be imputed. Parents, grandparents, and other relatives that were not descendants, were genotyped at high-density, low-density, or extremely low-density, and associated costs and imputation accuracies were evaluated.ResultsImputation accuracy and cost were influenced by the alternative genotyping strategies. Given the mating ratios and the numbers of offspring produced by males and females, an optimized low-cost genotyping strategy for a commercial pig population could involve genotyping male parents at high-density, female parents at low-density (e.g. 3000 SNP), and selection candidates at very low-density (384 SNP).ConclusionsAmong the selection candidates, 95.5 % and 93.5 % of the genotype variation contained in the high-density SNP panels were recovered using a genotyping strategy that costs respectively, $24.74 and $20.58 per candidate.
Highlights
Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain
The objective of this research was to compare the effectiveness of imputation accuracy and the potential cost of alternative genotyping strategies for a commercial breeding program
The costs of initiating such a genotyping strategy in a new line of animals would be low because genotyping large numbers of individuals at high-density does not appear to be required once the male and female parents of the generation for which the strategy is implemented are genotyped at high-density
Summary
Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. Both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to explore the cost and imputation accuracy of several alternative genotyping strategies in pedigreed populations. Successful breeding programs based on genomic information rely on large numbers of animals that are both phenotyped and genotyped at high-density [1,2]. Imputation of high-density genotypes for large numbers of phenotyped animals has been shown to be effective in generating large datasets at lower cost Genotyping strategies for imputation generally involve genotyping some individuals in a pedigree at high-density, others at low-density, and in some cases not genotyping other individuals at all.
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.
