Using iXora for Haplotyping to Increase the Resolution of Trait Mapping in Avocado

Quantitative trait loci (QTL) mapping associates a phenotypic trait with a region of the genome. In standard QTL mapping, each marker locus is considered individually. Another approach is to associate the trait with haplotype blocks rather than individual markers. To this end, we have developed iXora (Identifying crossovers and recombining alleles), a robust and efficient method for extracting reliable haplotypes of a mapping population, including the parental haplotypes. Each allele in the progeny is assigned to a haplotype inherited from the parent, and this information is used to associate the parental haplotypes with traits in the progeny.

We apply the iXora phasing and trait association framework to the avocado Florida mapping populations from the crosses Simmonds x Tonnage and Tonnage x Simmonds. The increased resolution from phasing is employed to locate the trait locus controlling flower type. We show that flower type is determined very accurately by the haplotype in a specific region in one of the parents. We demonstrate that iXora is applicable even in the absence of a complete genome sequence, given an ordered set of markers along the linkage groups.

For the iXora algorithm and references, see http://researcher.ibm.com/project/3430