Abstract :
[en] Most researches on genetic variety evaluation in Vietnamese local chicken breeds have been based up to now on microsatellite markers (Cuc et al., 2011; Pham et al., 2013). Thanks to the genotyping of ~580,000 SNPs on 95 chickens, this study aimed to assess the genetic diversity in four Vietnamese local breeds (Mia, Mong, Ho and Dong Tao). Inbreeding was examined through the detection of runs of homozygosity (ROH; Curik et al., 2014). The ROHs are long stretches of homozygous genome that are likely to reflect autozygosity. Given that Ho chickens have a small effective population size, more inbreeding and consequently longer ROHs are expected. Conversely, Mia chickens, with a larger effective population size should show less consanguinity and shorter ROHs. As expected, Mia chickens led to less observed homozygosity and less ROHs than the three other breeds. Moreover, when ROHs were subdivided in different lengths, the proportion of individuals having at least one R OH longer than 5Mb was significantly higher in Ho (63%) than in Mia chickens (33%). Given that very long ROHs are particularly associated with recent inbreeding, it seems that many Ho chickens have consanguineous parents. However, no significant difference was observed between the four breed concerning the total length of long ROHs (> 5Mb). In conclusion, the analysis of ROHs reported less consanguinity in Mia than in Ho chickens. In each breed, some individuals are found more consanguineous than expected. This study also confirms that ROHs are a useful tool in inbreeding research.
