Abstract: In order to better protect and utilize the Hechuan black pigs, the geneitc diversity, kinship, inbreeding coefficient, family structure and selection signatures of Hechuan black pigs conserved population were explored in this study. The 50K SNP chip was used to analyze the SNPs in 58 healthy adult Hechuan black pigs conserved population. The effective population size, polymorphic information content, polymorphic marker ratios, expected heterozygosity, observed heterozygosity, effective allele numbers and minor allele frequency was calculated to analyze the genetic diversity of the conserved population. The identity by state (IBS) diatance matrix and runs of homozygosity (ROH) for each sample was calculated by Plink software and the genomic relationship G matrix was calculated by Gamatrix (V2) software to analyze the kinship of the conserved population. The population cluster analysis was calculated by Mega X (V10.0) software to analyze the family structure of the conserved population. Tajima's D and iHS methods were used to analyze the selected signal regions on the genome of Hechuan black pig population and explore potential candidate genes. The results showed that the effective population size, average polymorphic information content, polymorphic marker ratios, average effective allele numbers, minor allele frequency of the Hechuan black pigs conserved population were 4.2, 0.156, 0.534, 1.38 and 0.141 respectively, which indicated that the genetic diversity of Hechuan black pigs conserved population was relatively abundant. The average expected heterozygosity and observed heterozygosity were 0.255 and 0.271, which indicated that the conserved population has been differentiated. The average IBS genetic distance of 58 Hechuan black pigs was 0.199 2±0.042 9, and the average IBS genetic distance of 26 breeding boars was 0.176 7 ±0.048 4. The results of IBS genetic distance and G matrix both suggested that some individuals had closely relattionship with each other. A total of 2 246 ROH, gatherring in individuals with the most ROH by 1-10 Mb length (79.12%) and 40-50 (48.28%) numbers, were founded in the Hechuan black pigs conserved population.A total of 2 246 ROH fragments were found in the Hechuan black pig population. The number of ROH fragments with a length of 1-10 Mb accounted for the most(79.12%), and the number of individuals with 40-50 ROH accounted for the most(48.28%). The average inbreeding coefficient of conserved population was 0.175. The Hechuan black pigs conserved population includes 7 families with boars and 1 family without boars, and the number of individuals in each family were significantly different. Using Tajima's D and iHS methods, 192 and 303 significant selection signal regions were detected, which contained 193 and 331 candidate genes, respectively. Five candidate genes were detected simultaneously by Tajima's D and iHS. HVCN1 was associated with sperm motility and sperm cryotolerance. TRAF3IP1 and PER2 were associated with immune function. In general, the genetic diversity of Hechuan black pigs conserved population was relatively abundant. However, there was a greater risk of inbreeding among some individuals, and the number of individuals in each family was significantly different. The number of boars in some families is small, thus, there was a risk of ancestry loss in this families. In addition, during the adaptive evolution of Hechuan black pigs, the related genes of reproduction and immune traits were selected to a certain extent.

Key words: Hechuan black pigs, 50K SNP chip, genetic diversity, genetic structure, selection signatures