Abstract: The aim of this study was to identify and analyze the single nucleotide polymorphism (SNP) and screen the specific SNPs in Jinfen White pigs. In this study, the whole genome of 30 ear DNA samples from 9 male and 21 female Jinfen White pigs were resequenced. The GATK software was used to detect the mutation sites, and VEP software was used for SNPs classification and annotation. The genome resequencing data of its parents, including Mashen pig, Taihu (Erhualian) pig, Landrace and Large white pig, were integrated to detect the specific SNPs loci of Jinfen White pig based on allele frequency. The biological functions of the genes including SNP loci were annotated by enrichment analysis. The results of whole genome resequencing of 30 Jinfen White pigs showed that about 1 761.73 Gb Clean reads were obtained by sequencing and data filtering, among which the average values of Q30 reached 91.77%. The average sample alignment rate was 75.61%, the average coverage depth was 14.7 X. A total of 14 680 807 SNPs were identified after filtering, most SNPs were distributed on Chr1 and in the non-coding region of the gene. Subsequently, 87 366 specific SNPs of Jinfen White pigs were screened based on allele frequencies, most of which were located on Chr2 and distributed in the intron. In addition, the missense mutant SNPs located in the exon region belonged to 343 genes, which were significantly enriched in organelles, organelle components, intestinal immune, fatty acid degradation pathway, et al. The SNPs were analyzed and 87 366 specific SNPs loci were also screened through whole genome resequencing and bioinformatics techniques. This study will provide a research basis for the development of molecular markers, pure breed identification and molecular breeding of Jinfen White pigs.

Key words: Jinfen White pig, whole genome resequencing, SNP