Genome-wide association analyses for coat colour patterns in the autochthonous Nero Siciliano pig breed

Nero Siciliano (or Sicilian Black) is an Italian autochthonous pig breed reared in the Sicily island, mainly under extensive management systems. Nero Siciliano pigs are black (with black skin and black hair), but animals with white face or partially white face ("suino facciolo") can be registered to the breed herd book. Sometimes, other white patterns on extreme portions of legs could appear in this population. This study took advantage from the rare occurrence of pigs with white patterns in the Nero Siciliano population to carry out a genome-wide association study and comparative genome-wide Fixation index (FST) analysis to identify genomic regions that could affect coat colour variability (solid black vs white patterns over black) in this autochthonous pig breed. Analyses have been conducted on 66 Nero Siciliano pigs: 30 completely black and 36 black with white patterns. All samples have been genotyped for the KIT gene duplication and MC1R mutations, two genes well known to affect coat colours in pigs. Only pigs that did not carry any duplication of the KIT gene and were homozygous for the ED2 black dominant MC1R gene allele (n = 26 completely black and n. 22 with white patterns) were genotyped with the Illumina PorcineSNP60 BeadChip. The genome-wide analyzes identified on chromosome 2 a significant marker (rs81329493) associated with the coat colour white patterns in this breed. The homologous chromosome region in felids contains the gene responsible for the blotched tabby and striped coat colour patterns. Further studies, including a larger number of pigs, are needed to confirm this result and identify the causative mutation (s) affecting this coat colour diversity, which might be used to design a conservation programme in this breed aiming to maintain phenotypic homogeneity (i.e. solid black) that is typically associated with Nero Siciliano pigs. This study demonstrated how genetic diversity segregating in an autochthonous genetic resource can be explored to understand the genetic mechanisms affecting phenotypic traits in a livestock species.