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Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region

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Abstract

The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

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Acknowledgments

We would like to think Dr. Fred Bogott at the Medical Center, Austin of Minnesota for his excellent English editing of the manuscript. This work was supported by Guangxi Provincial Natural Science Foundation of China (NO. 2013GXNSFDA019013 to Dr. Yuying Liao).

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Authors and Affiliations

  1. Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi Institute of Animal Sciences, Nanning, 530001, Guangxi, People’s Republic of China

    Yuying Liao, Guodong Mo, Junli Sun & Fengying Wei

  2. Clinical Research Center, Guizhou Medical University Hospital, Guiyang, 550004, Guizhou, People’s Republic of China

    Dezhong Joshua Liao

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  1. Yuying Liao
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Correspondence to Dezhong Joshua Liao.

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Liao, Y., Mo, G., Sun, J. et al. Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region. Mol Biol Rep 43, 415–425 (2016). https://doi.org/10.1007/s11033-016-3976-0

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