Abstract
The Duroc × (Landrace × Large White) hybrid pig (DLY) is the most popular commercial pig used in the Chinese pig industry. DLY pigs are usually white but sometimes show colored phenotypes. Colored DLY pigs are not favored by slaughterhouses and retailers, thus causing certain economic losses to farmers in China. In this study, we first conducted a genome-wide association study and RNA sequencing to demonstrate that KIT variants are responsible for diversifying coat color phenotypes segregating in a DLY population. We then defined the precise sizes and locations of four duplications (DUP1-4), four candidate causative mutations at the KIT locus, in the pig reference genome using the whole-genome sequence data of representative colored individuals. The sequence data also enabled us to identify a list of new KIT alleles. By investigating the association between these new alleles and coat color phenotypes, we provide further evidence that DUP2 is another causative mutation for the solid white coat color in pigs. DUP1 (the KIT gene duplication), DUP2 and the splice mutation are all required for the manifestation of a solid white coat color. DUP4 had a more significant effect on the formation of the belt phenotype compared with DUP3. Given the necessity of DUP2 for the solid white coat color, we detected IN/IN homozygotes lacking DUP2 in Large White and Landrace pigs and found that French Landrace pigs had the highest frequency (8.98%) of IN/IN individuals. This study not only advances our understanding of the molecular mechanism of the color phenotype in pigs, but also establishes a simple and accurate method for the screening of KIT IN/IN homozygotes in Large White and Landrace that would cause colored DLY pigs.
Highlights
Coat color is one of the most visualized breed features of domestic pigs
We genotyped the 103 DLY pigs segregating for four coat color phenotypes using the Illumina 80K chip
These results support that KIT variants are responsible for the coat color phenotypes segregating in the DLY population
Summary
After long-term artificial selection, domestic pigs have formed diversifying coat color phenotypes (Porter, 1993; Legault et al, 1998), including black, red, white, spotted, brown, belted, two-end black, etc. MC1R variants are KIT Novel Alleles in Pigs responsible for the dominant black, black spotted, and red coat colors in both Western and Chinese pigs (Kijas et al, 1998, 2001; Fang et al, 2009). KIT variants determine the dominant white coat color in Western pigs (Johansson et al, 1996; Marklund et al, 1998). TYRP1 and EDNRB variants are responsible for the brown (Ren et al, 2010) and white belt coat colors (Ai et al, 2013) in Chinese pigs, respectively
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