Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

SIMPLE SUMMARY: Coat color is an important phenotypic trait of pig breeds, and a few genes are involved in its regulation. After long-term selection, pig breeds have formed diversified coat color phenotypes (e.g., black, red, white, spotted, brown, belted, two-end black, etc.). To date, several major genes affecting pig coat color phenotypes have been identified. In this view, recent studies suggested a new type of molecular marker known as retrotransposon insertion polymorphisms (RIPs). This marker is considered an ideal molecular marker, showing the potential to be used for population genetic analysis in pigs, with the possibility to be extended to other livestock animals as well. Here, we revealed 42 RIPs in 20 coat color genes in pigs, and some RIPs may be useful in distinguishing different breeds. ABSTRACT: The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.