Fine mapping of a QTL for white markings on chromosome 23 in Scandinavian Fjord horses.

Abstract

In Fjord horses, it is undesirable to have extensive white markings on the head or legs. White markings tended to be multifactorial pleitropic traits with phenotypic effects not solely restricted to coat colour but a variety of other syndromes which could have a negative impact on the horse. In this thesis, 328 Fjord horses underwent a GWAS for white markings based on 67k SNPchip data. Of these 328 horses, 19 had white markings on the head or body. This GWAS identified 2 regions on chromosome 23 with significant association to white markings. Following this, 16 horses, evenly split between cases and controls, underwent resequencing culminating in variant calling using the GATK and FreeBayes. Further analysis was carried out on the peaks identified in the GWAS, as well as regions containing known white marking genes. This further analysis comprised of differences in allele frequency, Weir and Cockerham’s Fst and variant annotation. No clear mutations were identified in a protein coding gene, however an association with U6 spliceosomal RNA were indicated following filtering on variant annotation.