Conclusion
Maintaining the genomic diversity of Chinese domestic chicken breeds is important for economic and cultural reasons. We found that the smallex situ conserved populations that are maintained in controlled environments retain less genetic diversity than populations conservedin situ. In addition, the transfer of conservation populations from their place of origin to another site results in genetic differentiation. This may be caused by genetic drift or adaptation. Finally, we identified the “genomic conservation unit” for all three chicken breeds and proposed that phylogenetic trees should be used to select valuable indi18viduals for breeding within a conservation program, based on breed-specific characteristics markers as well as genome-wide markers. The results of this study provide a basis for further optimization of conservation programs for domestic chicken breeds in China.