Abstract：Black bone chickens (Gallus gallus domesticus) are excellent indigenous chicken resources in China and commonly believed to have medicinal properties. The study on the genetic diversity and breed identification of the black bone chickens is of great significance for genetic conservation. For this study, the complete mitochondrial DNA D-loop sequences of 197 chickens from 5 breeds (Silkie, Dongxiang Blue-eggshell, Jinhu Black-bone, Yugan Black-bone and Zhu Si) were analyzed. The size of full-length chicken mtDNA D-loop of 5 black bone breeds were 1 231 to 1 232 bp, with a single-base deletion from the 859 bp site in the 1 231 bp sequences. A total of 27 variable sites that defined 18 haplotypes were identified. The average haplotype diversity, nucleotide diversity and mean number of nucleotide differences were 0.862±0.013, 0.005 80±0.001 07 and 7.137, respectively. The median network showed that genetic structure of the mtDNA haplotypes of black bone chickens were distributed across 4 clades (haplogroups): Clades A, B, C, and E. However, haplogroups were dispersed in different breeds, and the distribution of morphology and geographical pattern was not obvious. This study data suggested that genetic distance between Zhu Si and Silkie was longer than the other breeds, which verified that Zhu Si chickens were hybridized from fast-growing broiler as maternal line. Chinese black bone chicken had relatively lower genetic diversity and likely shared 4 common maternal lineages. The results could be used as a reference for preservation, improvement and identification of Chinese black bone chickens.
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