Abstract Jiangsu Province possesses a large number of excellent indigenous chicken (Gallus gallus domesticus) resources. These breeds have been selected for an array of traits including better meat quality, better resistance to disease, and better adaptability to intensive management systems making them good candidates for increased crossbred production. The objective of this study was to determine the genetic diversities and population structures of chickens that are traditionally raised in Jiangsu province. To address this question, the complete mitochondrial DNA D-loop sequence of 149 chickens from 5 native breeds (Black langshan, White langshan, Luyuan, Liyang, and Taihu) of Jiangsu province were analyzed . Sequences read lengths of the native breeds were 1 231 to 1 232 bp, with a single-base deletion from the 859 bp site in the 1 231 bp haplotype. A total of 33 variable sites that defined 19 haplotypes were identified. The average haplotype diversity and nucleotide diversity were 0.862±0.017 and 0.005 91±0.001 35. The median network showed that genetic structure of the mtDNA haplotypes of Jiangsu chickens are distributed across 5 clades (haplogroups): Clades A, B, C, D, and E. However, most of the individuals characterized in this study belonged to clades A and B. The analysis of molecular variance (AMOVA) showed that genetic differentiation indexes F-statistics (Fst) was 0.334 97(P＜0.01), genetic variation within and between populations accounted for 66.5% and 33.5% of the total genetic variation respectively. The results of this study indicated that Jiangsu chicken populations have relatively low nucleotide and haplotype diversity and likely share 5 common maternal lineages, but there were no obvious differentiation between them, and that some chicken populations may have been mixed with exotic lineage chickens. The results of the current study can be used as baseline genetic information for genetic conservation program and in breeding of Jiangsu chickens.
