Genetic diversity and population genetic structure of Cambodian indigenous chickens
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 conduct...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2022-06-01
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| Series: | Animal Bioscience |
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| Online Access: | http://www.animbiosci.org/upload/pdf/ab-21-0351.pdf |
| _version_ | 1828815581506174976 |
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| author | Theary Ren Mitsuo Nunome Takayuki Suzuki Yoichi Matsuda |
| author_facet | Theary Ren Mitsuo Nunome Takayuki Suzuki Yoichi Matsuda |
| author_sort | Theary Ren |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T10:47:29Z |
| format | Article |
| id | doaj.art-c185aafdd003462eb27d97ea1ac0e75f |
| institution | Directory Open Access Journal |
| issn | 2765-0189 2765-0235 |
| language | English |
| last_indexed | 2024-12-12T10:47:29Z |
| publishDate | 2022-06-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Animal Bioscience |
| spelling | doaj.art-c185aafdd003462eb27d97ea1ac0e75f2022-12-22T00:26:51ZengAsian-Australasian Association of Animal Production SocietiesAnimal Bioscience2765-01892765-02352022-06-0135682683710.5713/ab.21.035124815Genetic diversity and population genetic structure of Cambodian indigenous chickensTheary Ren0Mitsuo Nunome1Takayuki Suzuki2Yoichi Matsuda3 General Directorate of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh 12352, Cambodia Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, JapanObjective 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.http://www.animbiosci.org/upload/pdf/ab-21-0351.pdfclustering analysislarge-scale population genetic studymicrosatellitemitochondrial dna d-loop sequencephylogenetic tree |
| spellingShingle | Theary Ren Mitsuo Nunome Takayuki Suzuki Yoichi Matsuda Genetic diversity and population genetic structure of Cambodian indigenous chickens Animal Bioscience clustering analysis large-scale population genetic study microsatellite mitochondrial dna d-loop sequence phylogenetic tree |
| title | Genetic diversity and population genetic structure of Cambodian indigenous chickens |
| title_full | Genetic diversity and population genetic structure of Cambodian indigenous chickens |
| title_fullStr | Genetic diversity and population genetic structure of Cambodian indigenous chickens |
| title_full_unstemmed | Genetic diversity and population genetic structure of Cambodian indigenous chickens |
| title_short | Genetic diversity and population genetic structure of Cambodian indigenous chickens |
| title_sort | genetic diversity and population genetic structure of cambodian indigenous chickens |
| topic | clustering analysis large-scale population genetic study microsatellite mitochondrial dna d-loop sequence phylogenetic tree |
| url | http://www.animbiosci.org/upload/pdf/ab-21-0351.pdf |
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