GWAS Identifies a Region Containing the SALL1 Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses.

Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using standardized photographs of 96 horses. Each horse was ranked lightest to darkest within the cohort for phenotype by 3 blinded observers. A genome-wide association study utilizing the relative shade ranking as the phenotype and using 268 487 single-nucleotide polymorphisms (SNPs) genotyped using the Affymetrix Equine 670k array identified a single significantly associated region on chromosome 3 (P = 2.934 × 10-8). Analysis of whole-genome sequences for horses spanning the diverse range of chestnut color identified candidate SNPs within the coding sequence of the only gene in the region: SALL1. The function of SALL1 is largely unknown, though it is predicted to interact with the Hermansky-Pudlak Syndrome type 1 (HPS1) protein, which causes partial albinism in humans. However, with only one study suggesting a circumstantial influence of the SALL1 protein on pigmentation, additional work is needed to confirm this new coat color locus in larger populations and investigate the function of this protein for impacts on equine health.

Needs Assessment: What Are the Barriers to Use of Equine Genetic Testing?

Genetic testing offers precise and accurate data to horse owners concerning their horse's health and offers potential economic value increases of foal crops via genome-assisted selection. Despite availability of at least 96 commercially available markers, fewer than 20 are commonly used. This project seeks to identify the barriers to the incorporation of genomic tools in diverse equine operations. Based on studies examining public opinion of human medical testing, we expected that lack of genetic education and few industry requirements for testing may contribute to neutral or negative opinions regarding genomic tools for horses. We developed a 20 total question survey to capture demographic information such as facility size, type, and primary breed, as well as horse owner familiarity, use, and outlook regarding equine genetic testing. Question types included multiple choice, Likert-type scale, and open-ended response. Recruitment through county extension agents and breed organizations supplied a broad sampling of the Florida horse industry. Responses were collected from February through May 2019. Data showed that 25% of horse owners had genetically tested their horses (n = 60). Of these consumers, 80% rated the quality of their experience as "excellent" or "good" (n = 15). There was a significant positive association between genetic education and likelihood to genetically test. Most respondents (65%) were interested in receiving information regarding genetic testing. Study participants preferred to find materials on genetic testing through Web-based articles and veterinarians. Results of this study will provide researchers with critical knowledge of their audience's needs and a roadmap to tailor future educational resources.