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BMC Genetics

, 14:38

Statistical and computational genetics


BackgroundF2 resource populations have been used extensively to map QTL segregating between pig breeds. A limitation associated with the use of these resource populations for fine mapping of QTL is the reduced number of founding individuals and recombinations of founding haplotypes occurring in the population. These limitations, however, become advantageous when attempting to impute unobserved genotypes using within family segregation information. A trade-off would be to re-type F2 populations using high density SNP panels for founding individuals and low density panels tagSNP in F2 individuals followed by imputation. Subsequently a combined meta-analysis of several populations would provide adequate power and resolution for QTL mapping, and could be achieved at relatively low cost. Such a strategy allows the wealth of phenotypic information that has previously been obtained on experimental resource populations to be further mined for QTL identification. In this study we used experimental and simulated high density genotypes HD-60K from an F2 cross to estimate imputation accuracy under several genotyping scenarios.

ResultsSelection of tagSNP using physical distance or linkage disequilibrium information produced similar imputation accuracies. In particular, tagSNP sets averaging 1 SNP every 2.1 Mb 1,200 SNP genome-wide yielded imputation accuracies IA close to 0.97. If instead of using custom panels, the commercially available 9K chip is used in the F2, IA reaches 0.99. In order to attain such high imputation accuracy the F0 and F1 generations should be genotyped at high density. Alternatively, when only the F0 is genotyped at HD, while F1 and F2 are genotyped with a 9K panel, IA drops to 0.90.

ConclusionsCombining 60K and 9K panels with imputation in F2 populations is an appealing strategy to re-genotype existing populations at a fraction of the cost.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-14-38 contains supplementary material, which is available to authorized users.

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Autor: Jose L Gualdrón Duarte - Ronald O Bates - Catherine W Ernst - Nancy E Raney - Rodolfo JC Cantet - Juan P Steibel


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