43 A QTL for skull morphology in Arabian horses

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Domestication and selective pressures alter developmental pathways of mammals. The identification of genomic loci for skull morphology in particular can illuminate pathways controlling facial shape. Previous work in the dog identified QTLs for skull morphology and highlighted relationships formed during the development of distinct breeds of dogs from lupine ancestors through the direction of 6 loci across the genome. The Arabian horse is known for its unique concave facial profile in comparison to other equine breeds. We extracted DNA from blood and hair samples for 103 Arabian horses exhibiting diverse skull morphology and genotyped these with the Affymetrix Axiom Equine HD 670k array. Phenotyping was accomplished using 7 defined face measures from a defined protocol and summarized face shape variation using a principal component analysis. Utilizing these 2 principal component scores as skull morphology phenotypes, we performed a genome wide association study using 315,553 SNPs to identify significant preliminary QTLs for the strongest variation in facial morphologywithin this population. We used a linear regression model (PLINK v1.90b6.26) including quality filters for MAF >0.05 and genotyping rate of above 95%. Given the stratification of this population and diversity of subgroups within the Arabian breed, efforts to account for inflation were implemented using the genomic relatedness as a covariate in the linear model. Strong variation in head lengths were noted in the skull principal component 1 phenotype, independent from body size and skull length. Preliminary GWAs identified a promising locus on ECA 5, candidate base pair region: 27,578,838–27,848,837, (raw P = 1.421e-11, Bonferroni corrected P = 1.584e-7) despite strong population stratification across the diverse Arabian breed. Three protein coding genes were noted in this candidate region and further work will investigate these for potentially functional variants and improve phenotype accuracy by applying photo morphometics.