Vietnamese local chicken breeds. Genetic diversity and prioritising breeds for cvonservation

The overall goal of this study was to characterize the genetic diversity of the Vietnamese local chicken breeds and to identify population priorities for conservation. The specific aims were 1) to assess and explain the population genetic structure of the Vietnamese breeds, 2) to characterize the Vietnamese breeds in relation to the Chinese breeds and wild chickens, 3) to estimate conservation potentials for conservation priorities of the Vietnamese breeds, and 4) to define an optimal allocation of limited conservation funds to them. First genetic diversity within and between the Vietnamese breeds was analysed at the autosomal level using 29 microsatellites. A total of 353 individuals of nine Vietnamese local breeds and two breeds of Chinese origin were studied. The Vietnamese breeds were sampled from the northern and southern parts of Vietnam while the two Chinese breeds (NIAS Chinese breeds) have been kept at the National Institute of Animal Sciences, Hanoi. The results revealed a high level of diversity within Vietnamese breeds. Analysing the genetic structure using the software package STRUCTURE suggested an optimal clustering at K = 6. These groups encompassed four homogeneous clusters, one formed by the two Chinese breeds and the other three representing a single breed each: the Mekong Delta breed Ac, the South Central Coast breed Choi, and the Red River Delta breed Dong Tao. The six remaining breeds formed two additional admixed clusters. This finding indicates that sub-structuring of the Vietnamese chicken breeds is related to their geographical distribution. The two NIAS Chinese breeds are genetically distinct from the Vietnamese breeds. Mitochondrial DNA D-loop sequences were used to determine the degree of shared mtDNA haplotypes between the studied breeds. A 455-bp fragment of the mtDNA Dloop region was sequenced in 222 chickens of nine Vietnamese breeds and two NIAS Chinese breeds. As reference, a skeleton was created based on chicken mtDNA sequences taken from the Genbank which assigned clades to suggested regions of domestication in chickens. Haplotypes of the nine Vietnamese and two NIAS Chinese breeds were aligned together with these sequences. The mtDNA haplotypes formed eight clades. The majority of individuals of the two NIAS Chinese breeds grouped together in one clade. Although the Vietnamese breeds were distributed across all eight clades, most of them clustered in three main clades originating from Yunnan, South and Southwest China and/or surrounding regions. The differentiation of Vietnamese breeds from Chinese chickens was characterised. For this, as reference, data of 14 indigenous breeds from China (Reference Chinese breeds) and three Red Jungle Fowl populations (Gallus gallus gallus and Gallus gallus spadiceus) genotyped at the same microsatellite loci in a previous study were included. Analysing the genetic structure indicated that the Vietnamese breeds formed a homogeneous group separated from the other breeds (except for the Chinese Chahua breed). This finding provides additional evidence that the Vietnamese gene pool is genetically different from the Chinese gene pool even when a wider range of breeds is considered. Another analysis was also used to find the degree of uniqueness of the Vietnamese breeds relative to a set of three Red Jungle fowl populations. Compared to the reference Chinese breeds, the contribution of the Vietnamese breeds to the set of Red Jungle Fowl populations is lower. This suggests that the Vietnamese breeds are more closely related to the Red Jungle fowl populations than the reference Chinese breeds. The second objective of this thesis was to estimate the conservation potential of the Vietnamese breeds and to derive optimal allocation of conservation funds to maximize genetic diversity conserved between these breeds. The Weitzman approach for assessing alternative conservation strategies for genetic diversity between breeds was used. The approach combines genetic diversity assessed at the molecular level and extinction probabilities estimated by socio-economic factors to derive conservation priorities of breeds based on their conservation potential. To investigate an optimal allocation of conservation funds, three different models were applied. These models reflect the range of possible functions between costs and effects in typical conservation situations. Under the assumptions made it is expected that half of the genetic diversity of the Vietnamese breeds will be lost within the next 30-50 years if no conservation efforts are taken. Conservation potential of the Vietnamese chicken breeds varies considerably. The optimum conservation strategy to maximise genetic diversity between the Vietnamese breeds should prioritize the breeds with the highest conservation potential. Population priorities for allocation of conservation funds to the Vietnamese breeds do not depend on which cost model was used. The three local breeds Te, Dong Tao and Ac have the highest conservation potential and should be the prime candidates for conservation programs.