Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost

Genetics Selection Evolution

Research

Christian Maltecca¹  Yijian Huang¹  Matthew A Cleveland²  John M Hickey³ 

[1] Animal Science Department, North Carolina State University, Campus, Box 7621, 27695, Raleigh, NC, USA;Genus plc., 100 Bluegrass Commons Blvd., Suite 2200, 37075, Hendersonville, TN, USA;School of Environmental and Rural Science, University of New England, Armidale, Australia;

关键词: Single Nucleotide Polymorphism;    Selection Candidate;    Imputation Accuracy;    Genotype Imputation;    Genotyping Strategy;   

DOI  :  10.1186/1297-9686-44-25

 received in 2012-01-20, accepted in 2012-07-31,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Huang et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.