Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population

Abstract

Objective The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between FROH and FSNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix. Conclusion Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig.

Keywords

• genetic diversity
• molecular pedigree
• population structure
• single nucleotide polymorphism (snp) chip