Genetic Diversity and Phylogeny Pattern across Chongqing (China) Chicken Populations Using mtDNA D-Loop Sequences

In this study, we investigated the genetic diversity and phylogeny pattern in five chicken populations from Chongqing, China, using a part of mitochondrial DNA (mtDNA) D-loop sequences. The results revealed that the overall haplotype diversity ( Hd ) and nucleotide diversity ( Pi ) among the five chicken populations were 0.91646 and 0.01273, respectively. Forty-one polymorphic sites were identified within the 506-bp length of the mtDNA D-loop sequence in 239 animals. The Neighbor-Joining phylogenetic tree based on F ST values demonstrated that the five Chongqing local chicken populations are divided into three clusters. We discovered 35 haplotypes clustered into six mtDNA haplogroups (A, B, C, E, G, and Y). Among the haplogroups, haplogroup A had the highest frequency of approximately 54.3%, whereas haplogroups G and Y had the lowest frequencies of approximately 2.9% each. Furthermore, all the five populations carried multiple haplogroups. Haplogroups A, B and E were shared by all the populations. Mismatch distribution analysis showed that no population expanded, and pairwise comparison of the populations revealed that a significant divergence ( p < 0.05) existed among all the populations. The results of this study suggested that all the five chicken populations in Chongqing possessed a rich genetic diversity. The phylogenetic network demonstrated the existence of gene flows from commercial populations. This study provides theoretical basis for the conservation and further utilization of these populations.