Evaluation of genetic diversity and structure of Vietnamese goat populations using multi locus microsatellite markers

Goats are an important component of the Vietnamese livestock industry but little is known about their genetic diversity, differentiation and population structure. We evaluated genetic diversity of seven indigenous goat populations located in different provinces (CoVBV (Co goats from Ba Vi), (CoVSL) Co goats from Son La, CoVTH (Co goats from Thanh Hoa), CoVNT (Co goats from Ninh Thuan), CoVHg (Co goats from Ha Giang), BTVBV (Bach Thoa goat from Ba Vi) and BTVNT (Bach Thoa goats from Ninh Thuan)) and used microsatellite markers to assess the gene flow and population structure among them. The basic diversity measures viz. allelic diversity and heterozygosity were low in Vietnam goats as compared to West Asian and European goats. The overall mean FIS was significantly positive in Co goats (0.203) whereas it was only 0.003 in Bach Thao goats. Considerable genetic differentiation existed among goat populations from different provinces with the mean global FST, FIT and FIS estimated to be 0.083, 0.178 and 0.104 respectively. The phylogenetic tree constructed on pair-wise allele sharing distances revealed clustering of the two Bach Thao goat populations together. Among the Co goat populations, Son La (CoVSL) and Ha Giang (CovHG) clustered together distinctly while Thanh Hoa (CoVTH), Ba Vi (CoVBV) and Ninh Thuan (CoVNT) populations clustered intermediately. The results of multi-dimensional scaling plot of pairwise FST showed a similar picture except that Co-Ninh Thuan (CoVNT) was differentiated from other Co goat populations. When genotype assignment was performed at breed level, the percent correct assignment of Bach Thao goats (93.7%–96.2%) was consistently higher than Co goats (86.8%–88.1%) across the three evaluated methods. When genotype assignment at sub-population level was done, both Co (CoVNT) and Bach Thao (BTHNT) goat populations in Ninh Thuan province were assigned correctly while the percent correct assignment differed among goat populations from other provinces. AMOVA and Bayesian clustering analysis revealed the existence of significant sub-population structure and varying levels of admixture within Co goats among different provinces. The present study is the first report on genetic diversity and structure of indigenous goat populations raised in different provinces of Vietnam.