Screening And Identification Of Candidate Genes With Wrinkle Skin Traits For Xiang Pig

The Xiang pig with wrinkled skin?XPZ?was a variant from Congjiang Xiang pig in Guizhou Province.Its skin is densely wrinkled and the wrinkles on the buttocks are abnormal,and the skin is thickened,the elasticity is poor,the backfat is thin,and the hair is unevenly distributed.However,as the largest organ in mammals,the skin has many physiological functions,such as regulating body temperature,maintaining internal environment stability,and participating in metabolism and immune response.To explore the root causes of wrinkles in Xiang pig with wrinkled skins,genome resequencing of 5 Xiang pig with wrinkled skins and 6 normal Xiang pigs?XP?was performed,and 13 European pig?EUP?resequencing data were downloaded from public databases.The bioinformatics analysis method was used to reveal the cause of the formation of wrinkle phenotype in the pigs from the genome level.The research results were as follows:The histological study showed that the epidermis of the Xiang pig with wrinkled skins has thickened?P<0.05?,and the thickness is uneven and the edges were irregular.Collagenous fiber staining showed that the collagen bundle of Xiang pig with wrinkled skin was reduced,and the fiber arrange loosely and disorderly.Under the dyeing of elastic fibers,the root sheath of the Xiang pig with wrinkled skins into the dermis,and the elastic fibers at the junction with the epidermis are reduced,and the accumulation fracture occurs.In addition,compared with the skin of normal Xiang pigs and large white pigs,the diameter of hair bulbs in the hair follicles of Xiang pig with wrinkled skins increased?P<0.05?,the number of hair shafts increased?P<0.01?.Under the scanning electron microscope,the bundle of collagenous fiber in the Xiang pig with wrinkled skins was reduced,and the filaments arranged in disorder and appeared fractured accumulation,which was sparse.The above results suggest that the wrinkle of Xiang pig with wrinkled skins may be caused by skin collapse,which includes thickening of the epidermis layer,reduction of fiber bundles in the dermis layer and fracture accumulation.Genomic resequencing of wrinkled pigs and normal pigs,as well as database downloads of European pig resequencing data,yielded high quality data of 570.66 G.Structural variation analysis of 24 pigs was performed using Pindel and SoftSV software,and 25,679 high-quality structural variants were identified,which affected the genome length of 17.78 Mb.A random selection of 30 structural variants for PCR validation showed that these 30 structural variants existed in the genome.In order to further analyze the differences in structural variation between Xiang pig with wrinkled skins and normal Xiang pigs and European pigs,the three were compared with each other.The unique structural variations of the Xiang pig with wrinkled skins,normal Xiang pigs and European pigs were 1242,4440 and 1341,respectively,and the unique structural variations of the three populations were not identical on the chromosome.Further analysis of the unique structural variation of the wrinkled pigs,1,242 unique structural variations affect the genome sequence of about1Mb,and the structural variation occurs less fragment.These unique structural variations are not consistent in the distribution density on chromosomes,and there are many structural variations in chromosomes 15 and 16.The VEP annotation results showed that 1,242 unique structural variations affected 443 genes,and only 5 genes had structural variations in the coding region.GO and KEGG functional analysis showed that pathways related to skin development are mainly related to the synthesis of extracellular matrix?ECM?components,such as glycosaminoglycan biosynthesis-heparan sulfate/heparin?ssc00534?,glycosaminoglycan biosynthesis-Synthesis of biomacromolecules such as keratan sulfate?ssc00533?,glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate?ssc00532?.ECM acts as an extracellular scaffold,and skin wrinkles of wrinkled skin pigs are caused by collapse of extracellular scaffolds.In order to further explore the influence of structural variation on the wrinkle traits of Xiang pig with wrinkled skin,seven genes affected by structural variation were screened as candidate genes.XYLT1-I10-_SV2268,GALNTL5-E4-_SV1425,JAK1-I1-_SV294,IGF1-I3-_SV302,FUT8-I6-_SV858,ALG12-_SV86,WIF1-I8-sv889,CHST7-I1-_SV160 eight structural variants have polymorphisms in the genome.Compared with normal Xiang pig?XP?and Large White pig?LG?,Xiang pig with wrinkled skin XYLT1-I10-_SV2268,JAK1-I1-_SV294,FUT8-I6-_SV858,ALG12-_SV86,WIF1-I8-sv889,IGF1-I3-_SV302 the D allele frequency was dominant in the six structural variants of?P<0.05?.Using RegRNA2.0 to predict the transcriptional regulatory elements in eight structural variants,all the seven structural variants contained transcriptional regulatory elements,FUT8-I6-_SV858 structural variation has up to 58 transcriptional regulatory motifs.The UCSC analysis found that seven structural variants contained repeats?TEs?and six structural variants contained SINE/tRAN elements.The GALNTL5-E4-_SV1425locus contains exon 4 of the gene,resulting in exon skipping of the gene.The mRNA expression of 8 candidate genes in the skin showed that except for JAK1 gene,the expression of DD deletion type of the other seven genes was significantly lower than that of normal type II?P<0.05?.These results suggest that structural variations of XYLT1-I10-_SV2268,JAK1-I1-_SV294,FUT8-I6-_SV858,ALG12-_SV86,WIF1-I8-sv889,IGF1-I3-_SV302,GALNTL5-E4-_SV1425,CHST7-I1-_SV160 may be associated with wrinkled skin,it is related to the formation of Wrinkle Skin traits for Xiang Pig.In summary,this study reveals the structural characteristics of wrinkled skin of Xiang pig with wrinkled skins from histologically.At the same time,the second generation of sequencing technology was used to re-sequence the genome of Xiang pig with wrinkled skins to construct a structural variation map of Xiang pig with wrinkled skins.The distribution characteristics of the unique structural variation of Xiang pig with wrinkled skins obtained eight structural variations related to the formation of skin folds,and were identified,which is of great significance for the analysis of the formation of wrinkle traits of Xiang pig with wrinkled skins.