Characteristics Of Sequence And Function Of The Hot Spot From ChrX Structural Variation In Xiang Pig

Xiang pig is a unique local pig breed with many special phenotypes in Guizhou province,but the structural characteristics of the Xiang genome are not yet clear.The present paper focused on the structural variation(SV)of chromosome X based on whole genome resequencing datasets of Xiang pig.The aligned reads in chrX were extracted from the results of six Xiang pig by using the second generation sequencing technology.The SVs in chrX were much more rich in Xiang pig breeds compared with that of other seven pig breeds.A total of 1605 SVs were detected out and 53 of those were specific in Xiang pigs,which was about two times higher than that of the other breeds.There were four types of SVs,deletion,insertion,inversion and tandom duplication,in which deletion type of variation with 1474 SVs was dominant in the chrX of Xiang pig.One of most important finding was that a specific hot spot region in Xiang pig was found out from the location of chrX:40866906-55257014 spanned about 14.4 Mb.The hot spot region of SV contained 213 SVs with 600 kb distance between the neighbored SV sits.Of 213 SVs,24 SVs was specific in Xiang pigs and disturbed nine genes,which were DGKK,pHF8,KLF8,AR,OpHN1,STARD8,PFKFB1,NBDY and PJA1 genes.These genes fell into the several pathways including Oocyte meiosis,chromatin modifying,AMPK signaling pathway,Adaptive Immune System based on GO and KEGG analysis results.It suggested that these SVs could be taken as candidate marks for the individual recognition and trait selection for Xiang pig.There were six SVs chosen from the hot spot regions of SV and proved to be present in pig populations using PCR method,which included SMC1A-I15-sv320,TRO-E12-sv108,KLF8-I3-sv322,KLF8-I6-sv103,DGKK-I2-SV119 and AR-I2-sv1872 sites.Furthermore,the SNP pattern in the hot spot region of SV were investigated using our compiled scripts together with several Bioinformatics programs.There got total of 99924 SNP sites shared between the chromosomes X of Xiang and Yorkshire pig breeds.And most of SNP sites took high Fst scores in the regions of 0.97-0.99.It indicated that the DNA sequences and genes in the hot spot regions of SVs were underwent a high selection pressure in the region of chrX:40866906-55257014 in the adaptive evolution process of Xiang and Yorkshire pig breeds.It resulted in the distance and differentiation between two pig breeds.In conclusion,the results supplied a foundation for the utility and understanding of genetics related with traits of Xiang pig.