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

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Abstract

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 FST 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.

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Funding

This work was supported by the Innovation Team Building Program in Chongqing universities (CXTDG201602004).

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Authors and Affiliations

  1. College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Southwest University, 400715, Chongqing, China

    X. Yang, G.-X. E, B.-G. Yang, C.-L. Liu, Y. Guo, Y. Gong & M.-H. Li

  2. Sichuan Animal Science Academy, 610066, Chengdu, Sichuan, China

    X. Yang

  3. Chongqing Agriculture and Rural Affairs Committee of Tongnan, 402660, Chongqing, China

    B.-E. Chen

  4. Dazhou Animal Husbandry Technology Extension Station, 635000, Dazhou, Sichan, China

    D.-P. Zhang

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Contributions

X.Y., G.X.E., B.G.Y., C.L.L., Y.G., and Y.G. contributed equally to this study. M.H.L., G.X.E., X.Y., C.L.L., B.G.Y., H.Q.H., Y.M.H., W.Y.Z., D.P.Z., Y.Y. and B.E.C. conceived and designed the experiments. X.Y., Y.G., B.G.Y., and Y.G. analyzed the data. G.X.E. and X.Y. wrote the paper. M.H.L. provided funding. All authors read and approved the manuscript.

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Correspondence to M.-H. Li.

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Conflict of interest. The authors declare that they have no conflicts of interest.

Statement on the welfare of animals. The animal experiment was approved by the Laboratory Animal Ethics Committee Southwest University.

Informed consent was obtained from all individual participants included in the study.

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Yang, X., E, GX., Yang, BG. et al. Genetic Diversity and Phylogeny Pattern across Chongqing (China) Chicken Populations Using mtDNA D-Loop Sequences. Russ J Genet 58, 1007–1016 (2022). https://doi.org/10.1134/S1022795422080117

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