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Abstract :
[en] Introduction
Local chicken breeds in Vietnam make up approximatively 85% of the national poultry population. Although these breeds are largely present, their productivity is low and their use is nowadays threatened by the massive importation of foreign productive breeds. In that changing context, conservation programs targeting several emblematic breeds have been set up. The goal of these programs is to characterize the endangered breeds and to keep a pool of characteristic animals in order to preserve this genetic heritage. Our contribution in these programs is a fine characterization of 4 local breeds at the genomic level.
Material and methods
95 animals from 4 breeds (32 Dong Tao (DT), 27 Ho (HO), 18 Mhong (MN) and 18 Mia (MA)) have been sampled in various farms from the Red River delta region in Vietnam. DNA has been extracted and genotypes have been obtained using the 500K Affymetrix SNP chip. Classical population diversity measures (Fst, PCA) have been calculated, and genomic inbreeding measures at the global and local genomic scales have been obtained.
Results
Although geographically very close, DT and HO breeds are clearly different at the genomic scale. Both breeds also differ from MN and MA, these last two breeds looking more similar. Some individuals provided some evidence of breeds intercrossing, while others could be considered as purebred. Genomic inbreeding measures reveal high level of homozygosity in all the 4 breeds, with inbreeding coefficients commonly comprised between 10% and 20%. Analyses using inbreeding age classes also reveal that the buildup of the current inbreeding is due to recent to very ancient (several thousand generations) contributions.
Conclusion
The observation of clear differences at the genomic level supports the presence of distinct breeds, although the occurrence of crossbred animals in an assumed purebred sample triggers the potential need of genomic tools to unambiguously identify the breed of these animals. High levels of inbreeding also deserves attention for the creation of future nucleus to be used for breeds conservation.
This work has been funded by the AI-VNUA institutional support program of ARES.
