Using Genomic Relationships to Identify Haplotypes

Current genomic methods using markers rely on linkage disequilibirum (LD) with quantitative trait loci (QTL) to identify genomic regions associated with traits.  Using haplotypes rather than markers could more accurately represent the QTL in a region.  Identification of haplotypes in a population currently relies on pedigree information or uses frequencies of shared alleles.  We propose a method that requires only SNP information by identifying individuals that have no to few mismatching homozygotes for a given region.  Individuals that share a haplotype will not have any such mismatches unless due to genotyping error.  After identifying such individuals we use clustering to assign haplotypes to the entire population.  This method was able to correctly identify the haplotypes in simulated data sets.