Abstract:

Aims: Southwest China is characterized by complex topography, diverse ecological conditions, and abundant indigenous chicken genetic resources. A systematic evaluation of the genetic diversity of local chicken populations in this region, together with potential introgression from exotic commercial breeds, is essential for the conservation and sustainable utilization of these valuable genetic resources. 

Methods: In this study, 21 representative indigenous chicken breeds from Chongqing, Sichuan, Guizhou, Yunnan, and Tibet, together with commonly used commercial chicken breeds, were investigated. The complete mitochondrial DNA control region (D-loop) was amplified and sequenced, and the resulting sequences were used to assess genetic diversity, haplotype composition, phylogenetic relationships, and potential maternal introgression from commercial breeds. 

Results: A total of 1,146 complete D-loop sequences were obtained. The overall haplotype diversity (Hd) and nucleotide diversity (π) were 0.943 and 0.00699, respectively, indicating a relatively high level of maternal genetic diversity across indigenous chicken populations in Southwest China, although diversity differed among breeds. Tajima’s D values for Daweishan Mini Chicken and Pingwu Red Chicken deviated significantly from neutrality, suggesting possible selection or demographic events. In total, 70 polymorphic sites and 105 haplotypes were identified, which were assigned to seven haplogroups (A, B, C, D, E, F, and G), with haplogroups A, B, and E being dominant. Phylogenetic and median-joining network analyses showed that the haplogroups formed relatively independent lineages, and that the genetic relationships among populations were more closely associated with dominant haplotype composition than with geographic distribution. Several haplotypes were widely shared among breeds and regions, indicating complex historical differentiation and gene flow. All commercial breeds belonged to haplogroup E. Except for Chahua Chicken and Dulong Chicken, all indigenous breeds contained varying proportions of haplogroup E haplotypes and shared core haplotypes with commercial breeds. In several populations, the proportion of haplogroup E was relatively high, suggesting possible maternal introgression from exotic lineages. 

Conclusion: Indigenous chickens in Southwest China still retain abundant maternal genetic variation overall. However, the elevated proportion of haplogroup E in some populations indicates that maternal genetic structure may have been influenced by exogenous commercial lineages. Strengthening the standardized management of conservation populations and carefully regulating the introduction of exotic bloodlines will therefore be important for maintaining genetic diversity and lineage integrity. These findings provide an important molecular genetic basis for the scientific conservation and rational utilization of indigenous chicken resources in Southwest China.

Key words: Southwest China, indigenous chickens, genetic diversity, mitochondrial DNA, D-loop region