Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers

Abstract

We use publicly available methods to impute missing genotypes, infer haplotypes and partition haplotypes into blocks for large numbers of single nucleotide polymorphic data on two sections of chromosomes. Haplotype trend regression was used to associate these haplotype blocks with a continuously distributed trait. A number of significant regions of chromosomes, that were not found when tested with single-marker tests, were identified. This study demonstrated a feasible framework to fine-mapping QTL using haplotypes of SNP markers.