Dissecting The Genetic Architecture Of The Congenital Hairless Phenotype In Large White Pigs

Innate hairless pigs provide an ideal animal model for deciphering the genetic mechanism of human pelada,as well as clinical test for human skin drugs and cosmetics.Up to now,there are only few hairless pigs available.The reported one includes the Mexican hairless pigs,of which the molecular mechanism still remains elusive.In this study,we applied a battery of genetic analysis to dissect the genetic mechanism underlying congenital hairless in a Large White pig population,with the aim to reveal the mechanisms of follicle formation and cycling development,and to provide an effective technique for the breeding of hairless pigs.First,we analysed the segregation of hairess phenotype in pedigree,and deduced that the congenital hairless phenotype in the Large White population was caused by a recessive and rare mutation on autosomes.Then we genotyped 149 pigs including 89 hairless individuals and 60 normal individuals from this Large White population using porcine 60K SNP chips,A genome-wide association study(GWAS)was conducted to map the underlying loci using a case/control model.We observed a strong association signal on chromosome 15,and the most significantly associated SNP ASGA0083771(P-value=2.04×10-35)locates at 113.78 Mb on this chromosome.All hairless individuals shared a large haplotype of 14.62 Mb harboring ASGA0083771.To refine the location of the causal locus,we performed the haplotype sharing analysis in global pig breeds,linkage disequilibrium analysis and genetic differentiation analysis around the ASGA008377)region.The 60K SNP data of 1194 pigs from 56 breeds were explored to reconstruct haplotypes of the ASGA0083771 region.A 1.83 Mb(113.37-115.20 Mb)haplotype was found exclusively in all hairless Large White pigs.In the linkage disequilibrium analysis,we defined the confidence interval of the causal locus into a 1.47 Mb(113.67-115.14 Mb)segment by searching SNPs having r2 values of greater than 0.8 with ASGA0083771.We also explored whole-genome sequence data of 3 hairless and 64 normal Large White pigs to calculate the genetic differentiation(Fst)scores between the two groups around the ASGA008377]region.We detected a strong genetic differentiation signal within a 1.7 Mb region(113.48-115.18 Mb)overlapping with the mapped region.Altogether,we focused on the 1.47 Mb overlapping region 114.67-115.14 Mb for further analysis as it is the most likely confidence interval of the hairless phenotype.To ultimately identify the causative gene and mutation,we constructed a neighbor-joining phylogenetic tree of all individuals used for the GWAS,and selected three hairless individuals and two normal individuals from different sub-populations.These five individuals were whole-genome resequenced at 20x coverages.Next,we searched all variants that showed concordant genotypes with the deduced genotypes of these five individuals,within the 1.47 Mb region.The filtered variants were further searched against the data set of genome sequence of 221 Chinese indigeness pigs and 402 Chinese and European pigs to identify rare variants with minor allele frequencies of less than 0.05.As a result,only one SNP was identified,which is located in the MAIP1 gene and alter Arginine to Cystine.To obtain additional evidence for the causality of HLSNP_C>T,we added this SNP into the 60K SNP data set,and reconducted the GWAS for the hairless phenotype.HLSNP_C>T appeared to be the most significantly associated SNP(P-value=6.17×10-85),when conditional on the effect of HLSNP_C>T,no association signal was detected.This SNP is eo-segregated with the hairless phenotype in the Large White population.These findings collectingly support the casualty of HLSNP_C>T.MAIP1 is an essential interaction protein from AAA family,which regulate almost all the activities of life.Mutations in BCS1L,one member of the AAA family lead to Bjomstad syndrome,which shows hear loss,hair abnormality or entire hair deficiency.We speculate that MAIP1 protein could interact with the AAA family proteins to regulate the periodic growth of hairs in pigs which need further investigations.