Whole Genome Resequencing Of Ningxiang Pig And Its Specific Marker Screening

Ningxiang pig is one of the excellent Indigenous pig breed in China,and it has superiority characteristics,including better disease resistance,strong adaptability and excellent meat quality.And its intramuscular fat content is up to 5.57%,which is much higher than foreign pig breeds.Also,Ningxiang pig often used as a dam to hybridize with foreign breeds.But the research on the excellent germplasm characteristics of Ningxiang pig is not deep enough,especially the regulation mechanism of genomic characteristics and intramuscular fat traits of Ningxiang pig needs to be resolved.In this study,the whole genome sequencing technology,bioinformatics analysis,structural mutation detection,X-linked scanning analysis and haplotype analysis,genetic diversity analysis were comprehensively used to research the genome-wide sequence of Ningxiang pig and its structural variation characteristics.Also screen the specific markers of Ningxiang pig by PCR.The results of the study are as follows:1.The PacBio Sequel platform and Illumina Hiseq platform were used for sequencing,and the genome of Ningxiang pig was assembled by BioNano Genomics Saphyr system and Hi-C approach.A highly contiguous assembly genome as demonstrated by the contig N50(～1Mb),scaffold N50(140.398Mb).2.Compared with the reference genome of Duroc pigs(Sus scrofa 10.2),we got 40 926 structural mutation informations by Pacbio mapping method.And a total of 6 738 genes were identified by annotation.DAVID analysis showed that these genes mainly related to lipid metabolism,glyceride metabolism,and glycerophospholipid metabolic pathways.3.X-linked sweep region comparative analysis between Ninxiang and Duroc pig.we identified 128 Mb and 126 Mb of syntenic sequences in Ningxiang pig and Duroc pig,respectively.And Collinearity in both regions of 0-48 Mb and 90–128 Mb segments can be clearly observed between two X-chromosomes.By comparing the SVs distribution on the X chromosome between the two cultivars,we found that the Ningxiang pig specific SVS was clustered in the 42 MB region from 48 MB to 90 MB.It has been annotated that all genes in this region are involved in reproduction and fat regulation of Ningxiang.4.We performed whole-genome resequencing to identified the genetic relationship ofNingxiang and download the resequencing data of other local pig breeds.Combining the resequencing data of 76 individuals of representing 18 geographically diverse breeds and two wild boar populations,a total of 25,542,115 SNPs were generated by mapping the reference genome.Based on these SNP informations,we constructed a neighbor-joining phylogenetic tree.The result indicated the Ningxiang and Shaziling pig are in the same subgroup,and Erhua pig and wild boar also cluster together.Principal Component Analysis(PCA)and Population Structure Analysis showed that there was gene exchange between Ningxiang pig,Shaling pig and Daweizi pig,and there is a close genetic relationship between Shaling pigs and Ningxiang pigs.5.compared the Ningxiang and Luchuan pig genome,we identified 42,812 Indels.With the DNA of Ningxiang pig,Lu Chuanzhu and Shaziling pig were used as templates,and identified the specific makers of chromosome 7 and chromosome 10 were identified by PCR and agarosegel electrophoresis,which can identified the Ningxiang pig from Lu Chuan and Shaziling pig.Anyhow,this study revealed the causes of the biological characteristics of Ningxiang pigs from the genomic level,also identified the latest genetic relationship with Ningxiang pigs,and screened the specific markers of Ningxiang pigs.This will provide a methodological basis for the identification of Ningxiang pigs and other pig breeds,at the same time,it lays a solid foundation for the identification,protection and meat traceability of Ningxiang pigs.