Discrepancies between Genetic and Visual Coat Color Assignment in Sarcidano Horse

Simple Summary Since horses were domesticated, human selection has introduced new coat colors and patterns, which have become a feature of added value in many current breeds. The wild population generally exhibit a basic coat color set (Bay, Black and Chestnut) due to a lack of crossbreeding with domestic breeds and mating with subjects carrying the same color set. Sometimes, visual identification of the coat color is difficult due to several individual and environmental conditions, leading to incorrect registration. However, it is crucial to identify coat colors accurately and to correctly report them in the Stud Book for legal and medical certification. Furthermore, Grays are horses born with an original basic coat color, but, gradually, hair graying leads to the complete loss of coat pigmentation with age. Therefore, it becomes very difficult to predict what color foals will be born from a Gray parent. Indeed, many other traits, like behavior, athletic skills, and genetic diseases, could be influenced by coat color. For breeders who want to produce foals with specific coats, this feature is also central. For all these reasons, molecular analysis of two major genes involved in the basic coat color definition (MC1R and ASIP genes) was conducted on 90 Sarcidano Horses, to correctly identify and assign individual coat colors.Abstract This study aimed to evaluate the discrepancies between genetic and visual coat color assignment in the Sarcidano Horse and to elucidate potential reasons. Individual DNA from 90 Sarcidano Horses was used for genetic assignment of coat color to explore the correspondence with individual forms containing phenotypical traits. The MC1R exon 1 and ASIP exon 3 have been genotyped and sequenced to obtain a picture of the coat color distribution in this breed. Surprisingly, once we compared the genetic results with the individual forms reporting the phenotypic data for each subject, a certain degree of non-correspondence between the phenotypic and genetic data in relation to coat color emerged. From the genetic analysis, Chestnuts (n = 58) resulted the most common Sarcidano Horse (n = 58), followed by a quite large number of Blacks (n = 28) and a very small number of Bays (n = 4), whereas phenotypic distribution resulted in 38 Chestnuts, 40 Bays, only 2 Blacks, and 10 Grays (without the possibility of recognizing the true color they carried). Chestnut resulted a very representative coat color, while many horses that visually identified as Bays were genetically Blacks. This discrepancy, that could be due to a variety of individual and external factors, including age, time of year, living situation and dietary condition, suggesting the importance of accurate coat color identification to ensure adequate features registration and reliable prediction of offspring's coat color.