Genetic diversity analysis of Thai indigenous pig population using microsatellite markers

OBJECTIVE: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. METHODS: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. RESULTS: The results showed that Thai pig populations had a high genetic diversity with mean total and effective (N(e)) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity (H(e)) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher H(e) compared to observed heterozygosity (H(o)) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei’s genetic distance, mean F (ST) estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. CONCLUSION: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.