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http://dx.doi.org/10.5713/ab.21.0351

Genetic diversity and population genetic structure of Cambodian indigenous chickens  

Ren, Theary (General Directorate of Animal Health and Production, National Animal Health and Production Research Institute)
Nunome, Mitsuo (Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University)
Suzuki, Takayuki (Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University)
Matsuda, Yoichi (Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University)
Publication Information
Animal Bioscience / v.35, no.6, 2022 , pp. 826-837 More about this Journal
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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1 Cambodia agriculture, natural resources, and rural development sector assessment, strategy, and road map. Manila, Philippines: Asian Development Bank; 2021.
2 Fumihito A, Miyake T, Sumi S, Takada M, Ohno S, Kondo N. One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc Natl Acad Sci USA 1994;91:12505-9. https://doi.org/10.1073/pnas.91.26.12505   DOI
3 Fumihito A, Miyake T, Takada M, et al. Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci USA 1996;93:6792-5. https://doi.org/10.1073/pnas.93.13.6792   DOI
4 Eriksson J, Larson G, Gunnarsson U, et al. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 2008;4:e1000010. https://doi.org/10.1371/journal.pgen.1000010   DOI
5 Miao YW, Peng MS, Wu GS, et al. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity 2013;110:277-82. https://doi.org/10.1038/hdy.2012.83   DOI
6 A value chain analysis of Cambodian smallholders' chicken production. Phnom Penh, Cambodia: PIN's Executive Reports Series; 2015.
7 Sonaiya F. Smallholder family poultry as a tool to initiate rural development. Poultry in the 21st Century; 2007 Nov 5-7; Bangkok, Thailand.
8 Mtileni BJ, Muchadeyi FC, Maiwashe A, Chimonyo M, Dzama K. Conservation and utilisation of indigenous chicken genetic resources in Southern Africa. Worlds Poult Sci J 2012;68:727-48. https://doi.org/10.1017/S0043933912000852   DOI
9 Granevitze Z, David L, Twito T, Weigend S, Feldman M, Hillel J. Phylogenetic resolution power of microsatellites and various single-nucleotide polymorphism types assessed in 10 divergent chicken populations. Anim Genet 2014;45:87-95. https://doi.org/10.1111/age.12088   DOI
10 Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines No. 9. Rome, Italy: Food and Agriculture Organization of the United Nations; 2011.
11 Cuc NTK, Simianer H, Eding H, et al. Assessing genetic diversity of Vietnamese local chicken breeds using microsatellites. Anim Genet 2010;41:545-7. https://doi.org/10.1111/j.1365-2052.2010.02039.x   DOI
12 Leroy G, Kayang BB, Youssao IAK, et al. Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa. BMC Genetics 2012;13:34. https://doi.org/10.1186/1471-2156-13-34   DOI
13 Roh HJ, Kim SC, Cho CY, et al. Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers. Asian-Australas J Anim Sci 2020;33:1896-904. https://doi.org/10.5713/ajas.19.0958   DOI
14 Hillel J, Groenen MAM, Tixier-Boichard M, et al. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet Sel Evol 2003;35:533-57. https://doi.org/10.1186/1297-9686-35-6-533   DOI
15 Osman SAM, Nishibori M. Phylogenetic analysis of South East Asian countries chickens based on mitochondrial DNA variations. J Poult Sci 2014;51:248-61. https://doi.org/10.2141/jpsa.0130190   DOI
16 Oka T, Ino Y, Nomura K, et al. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 2007;38:287-93. https://doi.org/10.1111/j.1365-2052.2007.01604.x   DOI
17 Embley TM. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol 1991;13:171-4. https://doi.org/10.1111/j.1472-765x.1991.tb00600.x   DOI
18 Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J Mol Biol 1990;212:599-634. https://doi.org/10.1016/0022-2836(90)90225-B   DOI
19 Bouckaert R, Heled J, Kuhnert D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014;10:e1003537. https://doi.org/10.1371/journal.pcbi.1003537   DOI
20 Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012;9:772. https://doi.org/10.1038/nmeth.2109   DOI
21 Earl DA, von Holdt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 2012;4:359-61. https://doi.org/10.1007/s12686-011-9548-7   DOI
22 Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000;155:945-59. https://doi.org/10.1093/genetics/155.2.945   DOI
23 Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 2013;4:98. https://doi.org/10.3389/fgene.2013.00098   DOI
24 Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 2015;15:1179-91. https://doi.org/10.1111/1755-0998.12387   DOI
25 Liu YP, Wu GS, Yao YG, et al. Multiple maternal origins of chickens: out of the Asian jungles. Mol Phylogenet Evol 2006;38:12-9. https://doi.org/10.1016/j.ympev.2005.09.014   DOI
26 Kusukawa N, Uemori T, Asada K, Kato I. Rapid and reliable protocol for direct sequencing of material amplified by the polymerase chain reaction. Biotechniques 1990;9:66-8.
27 Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, Yasue H. Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim Genet 2001;32:380-5. https://doi.org/10.1046/j.1365-2052.2001.00795.x   DOI
28 Cuc NTK, Simianer H, Groeneveld LF, Weigend S. Multiple maternal lineages of Vietnamese local chickens inferred by mitochondrial DNA D-loop sequences. Asian-Australas J Anim Sci 2011;24:155-61. https://doi.org/10.5713/ajas.2011.10155   DOI
29 Komiyama T, Ikeo K, Gojobori T. Where is the origin of the Japanese gamecocks? Gene 2003;317:195-202. https://doi.org/10.1016/S0378-1119(03)00703-0   DOI
30 Cuc NTK, Weigend S. Genetic relationship between Vietnamese chicken populations and chicken populations from different continents. Anim Vet Sci 2019;7:94-101. https://doi.org/10.11648/j.avs.20190704.12   DOI
31 Berthouly-Salazar C, Rognon X, Van TN, et al. Vietnamese chickens: a gate towards Asian genetic diversity. BMC Genet 2010;11:53. https://doi.org/10.1186/1471-2156-11-53   DOI
32 Kawabe K, Worawut R, Taura S, Shimogiri T, Nishida T, Okamoto S. Genetic diversity of mtDNA D-loop polymorphisms in Laotian native fowl populations. Asian-Australas J Anim Sci 2014;27:19-23. https://doi.org/10.5713/ajas.2013.13443   DOI
33 Hata A, Nunome M, Suwanasopee T, et al. Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens. Sci Rep 2021;11:2035. https://doi.org/10.1038/s41598-021-81589-7   DOI
34 Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 2012;28:2537-9. https://doi.org/10.1093/bioinformatics/bts460   DOI
35 Marshall TC, Slate J, Kruuk LE, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 1998;7:639-55. https://doi.org/10.1046/j.1365-294x.1998.00374.x   DOI
36 Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 2007;16:1099-106. https://doi.org/10.1111/j.1365-294X.2007.03089.x   DOI
37 Li Q, Zhang P, Li M, et al. Genetic diversity and relationship of Dulong chickens using mitochondrial DNA control region. Mitochondrial DNA B 2020;5:275-80. https://doi.org/10.1080/23802359.2019.1700837   DOI
38 Islam MA, Osman SAM, Nishibori M. Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region. Br Poult Sci 2019;60:628-37. https://doi.org/10.1080/00071668.2019.1655708   DOI
39 Sun H. The local chicken value chain in Cambodia: constraints and challenges of local chicken smallholder producers. Australasian Agribusiness Perspectives 2018;21:43-56.
40 Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52:696-704. https://doi.org/10.1080/10635150390235520   DOI
41 Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005;14:2611-20. https://doi.org/10.1111/j.1365-294X.2005.02553.x   DOI
42 Teinlek P, Siripattarapravat K, Tirawattanawanich C. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. AsianAustralas J Anim Sci 2018;31:804-11. https://doi.org/10.5713/ajas.17.0611   DOI
43 Watterson GA. Models for the logarithmic species abundance distributions. Theor Popul Biol 1974;6:217-50. https://doi.org/10.1016/0040-5809(74)90025-2   DOI
44 Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 2018;67:901-4. https://doi.org/10.1093/sysbio/syy032   DOI
45 Peng MS, Fan L, Shi NN, et al. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Mol Ecol Resour 2015;15:1238-42. https://doi.org/10.1111/1755-0998.12386   DOI
46 Nei M. Molecular evolutionary genetics. 1st ed. NY, USA: Columbia University Press; 1987.
47 Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 2017;34:3299-302. https://doi.org/10.1093/molbev/msx248   DOI
48 Dieringer D, Schlotterer C. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 2003;3:167-9. https://doi.org/10.1046/j.1471-8286.2003.00351.x   DOI
49 Fathi MM, Al-Homidan I, Abou-Emera OK, Al-Moshawah A. Characterisation of Saudi native chicken breeds: a case study of morphological and productive traits. Worlds Poult Sci J 2017;73:916-27. https://doi.org/10.1017/S0043933917000563   DOI
50 Dinesh MT, Geerlings E, Solkner J, Thea S, Thieme O, Wurzinger M. Characterization of indigenous chicken production systems in Cambodia. AHB - Promoting strategies for prevention and control of HPAI. Rome, Italy: Food and Agricultural Organization of the United Nations; 2009.
51 Vathana S, Keo S. Phenotypic characteristics of four indigenous chicken breeds in Cambodia. In: Proceedings of Tropentag Conference; 2006 Oct 11-13; Bonn, Germany.
52 Di Lorenzo P, Ceccobelli S, Panella F, Attard G, Lasagna E. The role of mitochondrial DNA to determine the origin of domestic chicken. World's Poult Sci J 2015;71;311-8. https://doi.org/10.1017/S0043933915000318   DOI