Transcriptome Of Bama Pig Skin Tissue Uncovers The Molecular Mechanism Underlying Coat Color Formation

Skin is the largest organ of body,and the main function of skin is to protect the underlying organs from possible harms of the external environment.Melanocyte plays an important role in skin.Bama pig has‘two-end black’phenotype,which could be a model to study connection between skin and melanocyte.To investigated mechanism implicated in‘two-end black’phenotype,the experiment investigated the relationship between mutations of MC1R,KIT and the‘two-end black’phenotype of Bama pigs.In addition,transcriptomic analysis was used to identify genes or study mechanism associated with absence of melanocyte.The result of sanger sequencing indicated that the mutation and SNP causing white skin was absent in Bama pigs.The MC1R haplotype E^D1（0201）was shared by Bama pigs and most Chinese pig breeds.Two haplotypes of the KIT gene（hap2 and hap8）were found in Bama pigs:hap2 was a haplotype with three SNPs（rs337128315 C>T,rs344308993 C>T,rs81508881 T>C）in exon 19 of KIT,and hap8 had two SNPs（rs344308993 C>T,rs81508881 T>C）in this same exon.The transcriptome analysis detected a total of 14,900 m RNAs and 7,549lnc RNAs were transcribed in the study.Results of cluster analysis and principal component analysis（PCA）demonstrated that expression of m RNAs and lnc RNAs varied greatly between two color skins.2,338 m RNA were identified as being differentially expressed,including 1,305 genes that were down-regulated in white skin and 1,033gene that were up-regulated in white skin.The genes down-regulated in white skin were associated with melanin synthesis,melanocyte-keratinocyte interaction and keratin,whereas the genes up-regulated in white skin were mainly associated with metabolism pathway,oxidative phosphorylation and citrate cycle（TCA cycle）.In addition,113 differentially expressed lnc RNAs were identified.Of these lnc RNAs,4 lnc RNAs might function in cell proliferation（TCONS＿00019024）,keratin synthesis（TCONS＿00077733）and cellar energy metabolism（TCONS＿00042201 and TCONS＿00060772）.Our results demonstrated that:（1）The mutation of MC1R,KIT that cause albino coat colour of pig were not detected in Bama pig.In addition,the haplotype of MC1R in Bama pig is in line with most Chinese domesticated pig.There were two KIT haplotypes in Bama pig.（2）Lack of melanocyte in white skin could contributed to differentially expression of numerous genes,such as coat color genes and keratin genes.（3）Keratinocyte might play an role in formation of‘two end black’phenotype.（4）Black skin and white skin might differ in energy metabolism,structure of hair and ability of scar formation.This research provided MC1R,KIT gene sequence information and Bama pig skin RNA datasets,and could accelerate the understanding of melanocyte loss.