A Genome-Wide Association Study Identifies Locus for Eye Color Variation in Puerto Rican Paso Fino Horses

The Puerto Rican Paso Fino is a gaited horse breed that segregates for iris color. The irises of Puerto Rican Paso Finos can vary from a dark brown color to a dynamic color breeders call “tiger” or “goat” eye. “Tiger” eye is characterized by shades of orange, yellow, and amber. Pedigree analysis implicated a recessive mode of inheritance for this phenotype. To map this trait and identify candidate genes for further investigation, a genome wide association study (GWAS) was conducted using an Illumina Equine SNP70 BeadChip and 24 unrelated DNA samples. To determine significant allelic associations, we used gPLINK (version 2.050) and applied an adaptive permutation approach to correct for multiple testing in this small sample set. The highest association detected was on ECA1 (P = 9.0x10^-6). The association of SNPs in two functional candidate genes from this region will be confirmed in a larger sample set (N=48). In addition these genes will be investigated further by DNA sequencing analysis.