Vietnamese chickens: a gate towards Asian genetic diversity

Abstract

Background: Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process.

Results: A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used.

Conclusions: In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.

Figure 1

Minimum spanning tree of the Vietnamese mtDNA haplotypes combined with the Chinese mtDNA from Liu et al. [7]. Circle size corresponds to haplotype frequencies. Haplotypes that are not found in the HG populations are in yellow, those that have been observed in wild populations are written in red. When haplotype is found both in the HG population, and in Chinese provinces, proportions are indicated

Figure 2

Multidimensional scaling plot constructed by K2P distances among Chinese breeds and the HG population. Colours correspond to province origin of the breed as in Figure 1.

Figure 3

The PhyML tree of all Asian breeds published data. Red branch indicate bootstrap values higher than 80%.

Figure 4

Distribution and proportions of haplogroups in Asian domestic and wild chickens. Ha Giang province is in blue.