Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse.

This research paper involves the study of the genetic factors that contribute to the percentage of white spotting, a characteristic feature, in the American Paint Horse breed. The researchers used digital photograph analysis and pedigree data to identify the influence of specific genetic factors on the coat color of the horses.

Collecting and Analyzing Data

• The researchers collected and analyzed digital photographs of 1195 registered American Paint Horses. In these photographs, they measured the depigmented (white) proportion of each horse’s coat.
• This photographic data was combined with genotype data provided by the American Paint Horse Association (APHA). The genotype data included information about nine genetic variations or polymorphisms associated with white spotting frequently found in Paint Horses. It also included information about two pigment-producing genes.

Correlation Between Genotype and Phenotype

• The researchers noticed a significant increase in the percentage of white coat in horses with more white-spotting alleles present, irrespective of the number of loci (fixed positions on genes) carrying these alleles. This information suggests that individual genetic variations related to white spotting have a strong additive genetic effect and interact with each other to produce the final phenotype.
• Furthermore, horses with a chestnut base coat color showed a higher white coat percentage. This observation provides evidence of an interaction between pigmentation signaling genes and white spotting loci.

Categories and Coat Color

• The APHA categorizes horses as either Regular or Solid Paint-Bred. The researchers found that these categories had a significant difference in their median white coat percentage, but the range of white coat percentage was similar. This analysis highlights the influence of the regional patterns of depigmentation on determining the phenotype.

Phenotype Prediction

• Models that predicted the white-coat percentage based on certain genotypes performed only moderately well. The researchers suggest that a larger sample size and more genotyped loci might be needed for more accurate predictions.
• The authors propose that in the future, models that enable phenotype prediction based on genotypes and automated phenotype assessments could improve the breeding process and member experience during the registration process at APHA.