Assessment of Maternal Genetic Diversity and Mitochondrial Population Structure of Endangered Indigenous Chicken Breeds in China

This study aimed to evaluate the maternal genetic diversity and mitochondrial population structure of once endangered indigenous chicken breeds in China under current conservation conditions. The genetic characteristics of six endangered indigenous chicken breeds, namely the Bian chicken, Jinyang Silky chicken, Pudong chicken, Xiaoshan chicken, Zhongshan Shalan chicken, and Pengxian Yellow chicken, were analyzed based on mitochondrial DNA (mtDNA) D-loop region sequences. Blood samples were collected from the wing vein. The D-loop region was amplified by PCR, and genetic characteristics were analyzed using bioinformatics approaches. A total of 368 individuals were amplified and sequenced, yielding complete D-loop sequences of 1231 and 1232 bp. Sequence alignment identified 42 polymorphic sites, with a hypervariable region primarily located between 167 and 446 bp. The overall haplotype diversity, nucleotide diversity, and the average number of nucleotide differences were 0.876 ± 0.010, 0.00603 ± 0.00012, and 7.426, respectively, with significant inter-breed variation. Haplotype analysis identified 32 haplotypes belonging to haplogroups A, B, C, E, F, and G. The proportion of breed-specific and shared haplotypes varied among breeds, and several high-frequency haplotypes were widely distributed across populations. Analysis of molecular variance (AMOVA) indicated that the majority of genetic variation occurred within breeds (83.41%), whereas among-breed variation accounted for 16.59% (Fst = 0.166), suggesting moderate population differentiation. The median-joining haplotype network exhibited a radial pattern centered on several core haplotypes, with no evidence of breed-specific clustering of maternal lineages. Neutrality tests (Tajima’s D and Fu’s Fs) yielded non-significant results, consistent with neutral evolution. However, mismatch distribution analyses suggested possible population expansion in the Zhongshan Shalan chicken and Pengxian Yellow chicken. In summary, the six endangered indigenous chicken breeds retain a moderate level of maternal genetic diversity under current conservation conditions. However, differences among breeds were observed in the maintenance of genetic diversity and population structure.