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https://hdl.handle.net/1959.11/14745
Title: | Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost | Contributor(s): | Huang, Yijian (author); Hickey, John (author); Cleveland, Matthew A (author); Maltecca, Christian (author) | Publication Date: | 2012 | Open Access: | Yes | DOI: | 10.1186/1297-9686-44-25 | Handle Link: | https://hdl.handle.net/1959.11/14745 | Abstract: | Background: Commercial 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. Methods: Pedigree 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. Results: Imputation 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). Conclusions: Among 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. | Publication Type: | Journal Article | Source of Publication: | Genetics Selection Evolution, v.44, p. 1-8 | Publisher: | BioMed Central Ltd | Place of Publication: | United Kingdom | ISSN: | 1297-9686 0999-193X |
Fields of Research (FoR) 2008: | 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) 070201 Animal Breeding |
Fields of Research (FoR) 2020: | 310506 Gene mapping 300305 Animal reproduction and breeding |
Socio-Economic Objective (SEO) 2008: | 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences | Socio-Economic Objective (SEO) 2020: | 280101 Expanding knowledge in the agricultural, food and veterinary sciences | Peer Reviewed: | Yes | HERDC Category Description: | C1 Refereed Article in a Scholarly Journal |
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Appears in Collections: | Journal Article |
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