Investigation of genomic variation of coat color genes in Italian goat breeds

Coat color, a distinctive trait described in the breed standards, allows the identification of many native and cosmopolitan breeds.The aim of this work is to evaluate the presence of signals of selection in genes involved in pigmentation processes of Capra hircus.Starting from genotyping data (GoatSNP50 BeadChip) of 423 goats belonging to 25 Italian breeds/populations provided by the Italian Goat Consortium. For every breed, an Integrated Haplotype Score (iHS) analysis was performed. Animals were then classified in 5 groups depending on their coat colors patterns (solid eumelanic, solid pheomelanic, pied eumelanic, pied pheomelanic and white). A reduced data set consisting of 467 SNPs included in regions surrounding 40 candidate genes (+0.25 Mb) was generated. Using this data set, a canonical discriminant and allelic frequencies analyses on the 5 groups previously defined were performed.The iHS, calculated with the Selscan software, allowed the identification of 44 relevant signal (>0.6) in 17 out of 25 breeds. These signals of selection are about 4% of all the genomic regions investigated, and fall in 26 genes. The canonical analysis highlighted that genes involved in the dilution of the eumelanins (e.g., OCA2 and MYO5A) and in the formation of the white patches (e.g., DOCK7 and PAX3) have a major role in differentiating these groups of breeds. The analysis of the allele frequencies of the 467 SNP was focused on extreme frequencies (<0.2 or >0.8) and allowed the identification of 13 genes with at least 67% of extreme SNPs in 8 different breeds. Another noteworthy result is the high level of extreme SNPs observed for the EDNRB gene (white patches) only in the Maltese population and in the Vallesana breed which are characterized by a wide white extension in their coat.In conclusion, the results show that, despite the lack of selection signals within breed likely due to a reduced standardization of coat color in goat, canonical discriminant analysis highlight the relevance of regions around genes involved in withe patches and eumelanin dilution. However, the pigmentation control in the species is a complex system that deserves to be better studied from a phenotypical/genomic point of view.