Epsilon Archive for Student Projects

Abstract

Hydrocephalus is an uncommon disorder in horses. However, hydrocephalus is observed more often in the Friesian horse breed than in other breeds. Due to the Friesian horse population has been closed for outside breeding and has a limited genetic pool. It leads to high rate of inbreeding. The general objective of this study is to get better understanding of genetic background of hydrocephalus in Friesian horses, which will be used to develop a DNA‐test using genetic markers for hydrocephalus in the Friesian horse breed. Genomic analysis based on case‐control study was performed on 20 cases and 47 controls. Data used in this study was provided by Faculty of Veterinary Medicine at Utrecht University, the Netherlands. Population stratification seems to be present between cases and controls because 55.2% of some cases and controls coming from different sires. This population structure was corrected using genomic control method. Hydrocephalus mutation in Friesian horses was found on one chromosome of the genome using genome‐wide association study (GWAS), indicating that it is a monogenic disorder. 68 associated SNPs based on genotype frequency differences included the 29 associated SNPs based on allele frequency differences between cases and controls were identified in this region. 85‐90% of affected Friesian horses were homozygous genotypes of unfavorable alleles for these following SNPs. Subsequently a haplotype association study was performed on the specific region. The result of this study showed that 54 associated haplotype blocks were also identified in the 29.3 Mb region. These haplotype blocks contained all associated SNPs that were found from GWAS. 228 genes were found in this region, but these genes were not the same as the identified genes of hydrocephalus in human and other species.