Analysis of the Genetic Diversity and Genetic Structure of Bamei Pig Population Based on Single-Nucleotide Polymorphism Chip

This paper assessed the genetic diversity, structure, and distance of Bamei pigs, a traditional Chinese indigenous breed, to conserve their genetic resources and facilitate comprehensive production planning. Using a 50K single-nucleotide polymorphism (SNP) chip, we genotyped 64 individuals from a Bamei pig conservation farm. Based on these data, we calculated genetic diversity parameters, constructed family structures, and identified runs of homozygosity (ROH) for each individual to obtain corresponding inbreeding coefficients. The results showed that the Bamei pig conservation population had an average genetic distance of 0.2707. The population maintained relatively rich genetic diversity, as indicated by a polymorphic marker proportion of 88.28% and observed (0.351) and expected (0.340) heterozygosity values that were very close. The inbreeding coefficient calculated based on ROH was at a medium level. The average inbreeding coefficient was 0.1302. Substantial inter-individual variation was observed, with some individuals showing relatively high inbreeding coefficients. Kinship analyses further confirmed the presence of close genetic relationships among certain individuals within the population and potential inbreeding risks. Family-structure analysis classified the boars into six families, with an uneven distribution of boars and sows both across and within these families. In order to ensure the continuous protection of the breed, it is urgent to optimize the breeding program. In the process of offspring retention, individuals with distant genetic relationships with boars and sows should be selected as much as possible, the inbreeding coefficient of the population should be gradually reduced, the number of families should be paid attention to, and the proportion and structural balance of each family should be paid attention to.