Genetic diversity and maternal origin of Vietnamese indigenous chicken breeds inferred from complete sequences of mitochondrial DNA D-loop region

Indigenous chickens play a significant role in food security, income growth and socio-cultural life of rural households in Vietnam. This study was conducted to assess the genetic diversity as well as the phylogenetic relationships of Vietnamese indigenous chickens (Gallus gallus) to support the conservation of their genetic resources for sustainable rural farming. In this study, the genetic diversity and the phylogenetic relationships of 10 Vietnamese indigenous chicken breeds were analyzed using complete sequences of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region. The average nucleotide and haplotype diversities of Vietnamese chickens were 0.006 3 ± 0.000 22 and 0.918 ± 0.010, respectively. A total of 39 polymorphic sites and 29 haplotypes were identified. The maximum likelihood tree classified these haplotypes into seven haplogroups (A, B, C, D, E, G and V), with haplogroups A and B being the two predominant maternal lineages of Vietnamese indigenous chickens, while haplogroups C, D, E, G and V were found in the remaining chickens. Several haplotypes from different haplogroups were shared among some chicken breeds. These results suggested that Vietnamese indigenous chicken breeds have multiple maternal origins, mainly from Chinese, Southeast Asian and Indian chickens, and that these breeds share common maternal lineages. The high level of genetic diversity in Vietnamese chickens demonstrates significance of conservation for future use.