Genome Wide Association Reveals That The Two-end-black Coat Color In Chinese Aboriginal Is Caused By The Interaction Of Major And Minor Effect Genes

Coat color is a breed characteristic in farm animals. Two-end-black coat color is one of representative coat colors in Chinese local pigs and the pig breeds are widely distributed in middle and lower areas of the Yangtze River in China. These pigs show black heads and hips and white belt bodies. So far, the molecular and genetic basis of the two-end-black phenotype remains elusive.In this study, four F2resource populations including Erhualian×Shaziling, Erhualian×Bamaxiang, Erhualian×Tongcheng and Erhualian×Rongchang were constructed. We genotyped all F0/F1/F2animals in these four resource populations using the porcine60K SNP chip and performed a genome-wide linkage analysis to identify the genetic loci underlying the two-end-black coat color. The phenotypes of F2animals showed continuous variation and were not consistent with the monogenic Mendelian inheritance, indicating that the two-end-black phenotype is a multifactorial complex trait. GWAS revealed that several significantly loci on SSC5, SSC11and SSC17were detected in all four resource populations. A meta-analysis of these resource populations identified the most significantly locus proximal to EDNRB on SSC11, suggesting that EDNRB is a major candidate locus affecting the two-end-black phenotype in pigs.When we fix the EDNRB effect in the farther GWAS analysis, several modifier genes effects at SSC5, SSC8, SSC17were identified. Among which gene EDN3adjacent the SSC17locus showed the most significant signal. By deep sequencing the EDN3gene, we found a1.6Kb IBD region shared by all Shaziling pigs and identified11diagnostic mutations distinguishing Shaziling from Erhualian and Duroc pigs. Further analysis by fixing the EDNRB and EDN3effects, we identified two other significantly loci on SSC5and SSC8in the Erhualian×Shaziling F2resource population. The two loci were adjacent to two coat color genes KITLG and KIT, respectively.This study showed that the two-end-black coat color is governed by a major gene (EDNRB) and several modifier genes including EDN3, KIT and KITLG. We speculate that EDNRB control the basic conformation of two-end-black coat color, and other modifer genes affect the extent of white belt and spot sizes. The genetic mechanism of Rongchang coat color is even more complex, which were involved with three major signaling pathway of melanocytes development. The results renewed our traditional understanding of coat colors as monogenic traits, and paved the load to ultimately identify the causal variants leading to the two-end-black phenotype in Chinese indigenous pigs.