Animal Bioscience

  • 제35권6호
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  • Pages.826-837
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  • 2022
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  • 2765-0189(pISSN)
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  • 2765-0235(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
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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)
  • 투고 : 2021.08.01
  • 심사 : 2021.11.29
  • 발행 : 2022.06.01
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초록

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.

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과제정보

We express our sincere gratitude to Toshiharu Tanaka and Il-Ryong Choi (Cambodia Campus, Asian Satellite Campuses Institute, Nagoya University), Vutha Pheng (Cambodia Campus, Asian Satellite Campuses Institute, Nagoya University, and National Institute of Agriculture and Technology Prek Leap, Phnom Penh, Cambodia), and Sotaro Chiba (Graduate School of Bioagricultural Sciences, Nagoya University) for supporting our study. We also express our appreciation to the National Animal Health and Production Research Institute, Ministry of Agriculture, Forestry and Fisheries, Cambodia, and the staffs of the Animal Health and Production offices in the 24 provinces in Cambodia for arranging sample collection and the farmers who provided chicken blood samples.

참고문헌

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. A value chain analysis of Cambodian smallholders' chicken production. Phnom Penh, Cambodia: PIN's Executive Reports Series; 2015.
  9. Sonaiya F. Smallholder family poultry as a tool to initiate rural development. Poultry in the 21st Century; 2007 Nov 5-7; Bangkok, Thailand.
  10. 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.
  11. Sun H. The local chicken value chain in Cambodia: constraints and challenges of local chicken smallholder producers. Australasian Agribusiness Perspectives 2018;21:43-56.
  12. 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
  13. 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
  14. Vathana S, Keo S. Phenotypic characteristics of four indigenous chicken breeds in Cambodia. In: Proceedings of Tropentag Conference; 2006 Oct 11-13; Bonn, Germany.
  15. 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
  16. 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
  17. 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.
  18. 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
  19. 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
  20. 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
  21. 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.
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Nei M. Molecular evolutionary genetics. 1st ed. NY, USA: Columbia University Press; 1987.
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. Cambodia agriculture, natural resources, and rural development sector assessment, strategy, and road map. Manila, Philippines: Asian Development Bank; 2021.