%0 Journal Article
%T Haplotype inference in crossbred populations without pedigree information
%A Albart Coster
%A Henri CM Heuven
%A Rohan L Fernando
%A Jack CM Dekkers
%J Genetics Selection Evolution
%D 2009
%I BioMed Central
%R 10.1186/1297-9686-41-40
%X 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.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.In general, marker genotypes of polyploid organisms are unordered, i.e. it is unknown to which of the two homologous chromosomes each allele at each marker belongs. The sequence of alleles at adjacent markers on one chromosome is called a haplotype; in diploid organisms a genotype consists of two haplotypes. Haplotypes provide information about the cosegregation of chromosomal segments and can be used to identify relatives when pedigree information is unknown. The haplotypes that an individual carries can be determined experimentally but this is expensive [1]. Alternatively, haplotypes can be inferred, either with or without pedigree information.When pedigree information is available, haplotypes can be inferred using genotype data of relatives (e.g. [2,3]). When pedigree information is not available, haplotypes can be inferred from genotype data of the population (e.g. [4,1-8]).Stephens et al. [1] used a Bayesian model to obtain a posterior distribution of haplotypes. Their prior distribution for haplotypes approximates a coancestry model by which distinct
%U http://www.gsejournal.org/content/41/1/40