Haplotype inference in crossbred populations without pedigree information Albart Coster1 , Henri CM Heuven1,2 , Rohan L Fernando3 and Jack CM Dekkers3 1Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands 2Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands 3Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, USA author email corresponding author email Genetics Selection Evolution 2009, 41:40doi:10.1186/1297-9686-41-40 The electronic version of this article is the complete one and can be found online at: http://www.gsejournal.org/content/41/1/40 Received: 3 February 2009 Accepted: 11 August 2009 Published: 11 August 2009 © 2009 Coster et al; licensee 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. Abstract Background Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called crossbreeding and hybridization in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals. Results We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population. Conclusion Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating
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