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Anim Biosci > Accepted Articles
https://doi.org/10.5713/ab.21.0351    [Accepted] Published online January 5, 2022.
Genetic diversity and population genetic structure of Cambodian indigenous chickens
Theary Ren1,2  , Mitsuo Nunome3,*  , Takayuki Suzuki3,4  , Yoichi Matsuda3,4,* 
1General Directorate of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh 12352, Cambodia
2Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan 
3Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
4Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
Correspondence:  Mitsuo Nunome,Email: mtnunome@agr.nagoya-u.ac.jp
Yoichi Matsuda, Tel: +81-52-788-6283, Fax: +81-52-788-4114, Email: yoimatsu@agr.nagoya-u.ac.jp
Received: 9 August 2021   • Revised: 9 September 2021   • Accepted: 29 November 2021
Abstract
Objective
Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide.
Methods
A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds.
Results
A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries.

Conclusion

Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.
Keywords: Clustering Analysis; Large-scale Population Genetic Study; Microsatellite; Mitochondrial DNA D-loop Sequence; Phylogenetic Tree


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