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 19^th 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 (<i>SLC45A2</i>) 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&gt;A and rs693695020:G&gt;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 <i>SLC45A2</i> 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.