Abstract:
Objective Genetic diversity and family structure of a preserved population of Pushi black pig were analyzed using the SNP bead chip for resource conservation.
Method SNPs of 79 adult Pushi black pigs consisting of 10 boars and 69 sows were determined using Porcine 50K SNP Beadchips. Software, including Plink, Gmatix, and Mega X, was used to analyze the genetic diversity and phylogenetic relationships to construct phylogenetic structure of the pig population.
Result A total of polymorphic 57466 SNP loci were found with an average genotype detection rate of 99.15%. The population showed evidence of inbreeding as the effective Ne was merely 1.5 and the average observed heterozygosity slightly below the expected level. The average distance of IBS was (0.2949±0.0726) and that for the boars (0.277 1±0.091 8). A total of (29.60±16.12) ROHs were detected with 40.5% of them between 0 and 100 Mb in length. The average inbreeding coefficient based on ROH was 0.108. The analysis on IBS distance matrix, G matrix, and population ROHs indicated a close genetic relationship among the individual animals. Based on the evolutionary tree, the population was divided into two families containing boars and one without.
Conclusion The population of Pushi black pigs under study had only a few families, which varied greatly in number of members in each family and showed a high degree of inbreeding. Consequently, introducing or creating new lineages to expand the gene pool and reduce inbreeding coefficient for the population seemed imperative.
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