Is KIT locus polymorphism rs328592739 related to white belt phenotype in Krskopolje pig?

Krškopolje pig is a local Slovenian breed with black coat and white belt of variable width over the shoulders. The breed experienced serious bottle neck effect in the middle of the 20th century followed by the introgression of different breeds, some of them with the goal to preserve belted phenotype. The belt allele was assigned to the KIT proto-oncogene receptor tyrosine kinase (KIT) gene. A number of single nucleotide polymorphisms (SNPs) and structural variations on of the KIT locus were observed. The synonymous SNP rs328592739 in the KIT gene was reported as a marker for distinguishing meat of belted Cinta Senese pigs from meat of non-belted breeds. In the present study, the SNP rs328592739 in Krškopolje, Cinta Senese and Swäbisch-Hall belted pigs has been genotyped using PCR-RFLP approach. In Krškopolje pig the region surrounding SNP rs328592739 was also sequenced using Sanger sequencing. In addition, publicly available whole-genome sequencing data for pigs of 12 different breeds and wild boar were analysed to obtain the sequence of KIT locus and its surrounding region in belted and non-belted pig breeds. The results show that SNP rs328592739 is not associated with white belt phenotype across different pig breeds. However, the analysis revealed structural variations within the KIT locus which may be associated with belted phenotype in pigs