Abstract：The Jiangxi province has numerous native domestic chicken breeds. This research aimed to characterize the genetic diversity and phylogeny of Jiangxi chicken (Gallus gallus domesticus) breeds. A total of 198 blood samples were collected from 6 breeds (Anyi Gray, Baier Yellow, Chongren Partridge, Silkie, Dongxiang Blue-eggshell, and Yugan Black-bone), reared in different areas of Jiangxi province. In this study, the PCR amplification method combined with nucleic acid sequencing technology was employed to detect the complete mitochondrial DNA (mtDNA) nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 6 (ND6) sequences. The results demonstrated that the full length of ND6 gene of 6 Jiangxi chicken breeds was 522 bp. A total of 7 variable sites were identified, which defined 7 haplotypes, Hap1 was the mainstream haplotype. The differences in nucleotide diversity, haplotype diversity, and the average number of nucleotide differences were 0.002 75 ± 0.000 86, 0.694 ± 0.024, and 1.437, respectively. The median network diagram exhibited that the haplotype of 6 Jiangxi chicken breeds presented a star-shaped divergent distribution. Phylogenetic analysis showed that Silkie, Dongxiang Blue-eggshell and Yugan Black-bone clustered into one branch, and Anyi Gray, Baier Yellow, and Chongren Partridge clustered into another branch. The mitochondrial ND6 gene polymorphism information of Jiangxi chicken breeds was abundant, black bone chickens may have a different maternal origin. The results of this study will provide a reference for the preservation, improvement, and identification of Jiangxi chicken breeds.
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