Revealing fine scale subpopulation structure in the Vietnamese H'Mong cattle breed for conservation purposes

Abstract

Background: During the last decades, there has been an acceleration of the loss of domestic animal biodiversity. For conservation purposes, the genetic diversity of the H'Mong cattle, an indigenous local breed was studied. Single-nucleotide polymorphisms (SNP) of the SRY gene and mtDNA D-Loop sequence were analysed to clarify the origin of the breed. The genetic diversity was assessed through genetic data with twenty-five FAO microsatellites, and morphometric data with five body measurements from 408 animals sampled from eight districts of the Ha Giang province.

Results: The SRY genes were all of the zebu type. Among the 27 mtDNA haplotypes, 12 haplotypes were of the taurine type and the remaining 15 of the zebu type. This indicates female taurine introgression in the zebu H'Mong. The observed and expected heterozygosity ranged from 0.616 to 0.673 and from 0.681 to 0.729 respectively according to district, with low genetic differentiation (F ST = 0.0076). Multivariate analysis on morphometric and genetic data shows a separation of districts into two groups following a south-west/north-east cline and admixture analysis confirmed the two clusters, but no differentiation of taurine introgression between clusters was observed. A possible admixture with the Yellow cattle breed from a neighbouring province was suggested through genetic data and householder interviews.

Conclusions: In this study we demonstrate the interest of fine-scale sampling for the study of genetic structure of local breeds. Such a study allows avoiding erroneous conservation policies and on the contrary, proposes measures for conserving and limiting crossbreeding between the H'Mong and the Yellow cattle breeds.

Figure 1

Map of the Ha Giang province: a) district borders (bold lines), b) commune sampled in grey light. See Table 1 for district codes.

Figure 2

Unrooted neighbour-joining tree of 304 cattle mtDNA D-loop sequences: European taurine breed (dark circle), Chinese taurine breed (grey circle), Admixed Chinese breed (Yellow square), HG population (dark square), Chinese zebu breed (red triangle).

Figure 3

Neighbour-joining tree of the 7 taurine and indicine breeds, and the two M'Hong subpopulations, based on DR distances and established with 1000 bootstraps on the loci (eight common microsatellites). Breed codes are given in Table 1.

Figure 4

Representation of the Ha Giang district H'Mong cattle populations using discriminant analysis (25 microsatellites + 5 morphometric traits) with the Hill & Smith procedure. This procedure similar to PCA allows maximising differentiation between districts using genetic and morphometric data. The first axis coincides with an east/west cline and separates the districts into 2 groups. See Table 1 for district codes.

Figure 5

Grid map of individual probabilities to belong to cluster 1 ranging from q < 0.03 in white to q > 0.96 in dark obtained by STRUCTURE using 25 microsatellites.