Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene

The Mangalitza lard-type pig breed is well known for its fatty appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main varieties were created in the 19th century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow Belly Mangalitza, and Red Mangalitza. The Swallow Belly variety has a black coat combined with yellow blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci which frequencies have been modified by artificial selection. Performance of selection scans, with hapFLK and BayeScan, and of a genome-wide association study for coat colour in Red, Swallow Belly and Blond Mangalitza pigs, highlighted the existence of one region on SSC16 (18-20 Mb) with potential effects on hair pigmentation. The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) gene. The polymorphisms of this gene has been associated with reduced levels or absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G>A and rs693695020:G>A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.