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Li J, Jiang J, Jin Q, Yuan Z, Qiu J. Mitochondrial DNA evidence reflects high genetic divergence of Amynthas aspergillum (Oligochaeta: Megascolecidae) in southern China. Ecol Evol 2024; 14:e11452. [PMID: 38826156 PMCID: PMC11140451 DOI: 10.1002/ece3.11452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Amynthas aspergillum (Perrier, 1872), a natural resource used in traditional Chinese medicine (Guang-dilong) with high economic value, is widely distributed in forests and farmland habitats in the hilly areas of southern China. To investigate the extent of genetic differentiation and diversity in A. aspergillum, a population genetic structure study was performed on 157 samples from 75 locations in southern China using the mitochondrial genes COI, COII, 12S rRNA, 16S rRNA, and NDI. The results indicated that A. aspergillum had a high level of genetic diversity, and variation within populations was the main source of the total variation. Six deeply divergent mitochondrial clades (I-VI) were detected using both phylogenetic tree and haplotype network analyses. This finding was supported by the high Kimura two-parameter genetic distance and the pairwise fixation index value obtained based on the COI gene. No significant phylogeographic structures were observed. The widespread geographic distribution of clades II, IV, and VI suggested a recent demographic expansion based on multiple analysis results. These results include a high level of Hd and low π, star-shaped haplotype network structures with a high number of less frequent haplotypes, significantly negative neutrality test values, and a unimodal mismatch distribution pattern. The divergence time estimates and reconstruction of the ancestral area revealed that A. aspergillum originated in Guangxi Province and underwent initial intraspecific diversification in the early Pliocene to generate clade I. Then, it gradually dispersed eastward and rapidly differentiated into clades II-V during the Pleistocene. The Yunnan-Guizhou Plateau and Nanling and Wuyi Mountains might act as geographical barriers for the spread of A. aspergillum to the west and north.
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Affiliation(s)
- Jiali Li
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jibao Jiang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qing Jin
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhu Yuan
- School of PharmacyShanghai University of Medicine & Health SciencesShanghaiChina
| | - Jiangping Qiu
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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Ediriweera TK, Manjula P, Kim J, Kim JH, Nam S, Kim M, Cho E, Bhuiyan MSA, Rashid MA, Lee JH. Identification of new major histocompatibility complex-B Haplotypes in Bangladesh native chickens. Anim Biosci 2024; 37:826-831. [PMID: 38419540 PMCID: PMC11065705 DOI: 10.5713/ab.23.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/18/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck. METHODS These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program. RESULTS A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes. CONCLUSION The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.
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Affiliation(s)
| | - Prabuddha Manjula
- Department of Animal Science, Uva Wellassa University, Badulla 90000,
Sri Lanka
| | - Jaewon Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Jin Hyung Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Seonju Nam
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Eunjin Cho
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
| | | | - Md. Abdur Rashid
- Poultry Production Research Division, Bangladesh Livestock Research Institute, Dhaka-1341,
Bangladesh
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
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Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985–4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467–2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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Kanakachari M, Rahman H, Chatterjee RN, Bhattacharya TK. Signature of Indian native chicken breeds: a perspective. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2026201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - H. Rahman
- Molecular Genetics and Breeding Unit, South Asia Regional Office, New Delhi, International Livestock Research Institute (ILRI), Nairobi, Kenya
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Ren T, Nunome M, Suzuki T, Matsuda Y. Genetic diversity and population genetic structure of Cambodian indigenous chickens. Anim Biosci 2022; 35:826-837. [PMID: 34991210 PMCID: PMC9066038 DOI: 10.5713/ab.21.0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
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.
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Affiliation(s)
- Theary Ren
- General Directorate of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh 12352, Cambodia.,Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Mon SLY, Lwin M, Maw AA, Htun LL, Bawm S, Kawabe K, Wada Y, Okamoto S, Shimogiri T. Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D-loop sequence reveals their characteristics as a genetic resource. Anim Sci J 2021; 92:e13647. [PMID: 34647390 DOI: 10.1111/asj.13647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023]
Abstract
Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.
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Affiliation(s)
- Su Lai Yee Mon
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Moe Lwin
- Research and Development Division, Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Aye Aye Maw
- Department of Genetics and Animal Breeding, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Saw Bawm
- Department of International Relations and Information Technology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Kotaro Kawabe
- Education Center, Kagoshima University, Kagoshima, Japan
| | - Yasuhiko Wada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Faculty of Agriculture, Saga University, Saga, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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Osman SAM, Nishibori M, Yonezawa T. Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens. Anim Biosci 2021; 34:941-948. [PMID: 32299160 PMCID: PMC8100483 DOI: 10.5713/ajas.19.0932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/20/2020] [Accepted: 04/09/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan. METHODS Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences. RESULTS This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1. CONCLUSION The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.
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Grants
- 22580319 Ministry of Education, Culture, Sports, Science, and Technology
- 26292139 Ministry of Education, Culture, Sports, Science, and Technology
- 19H00534 Ministry of Education, Culture, Sports, Science, and Technology
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Affiliation(s)
- Sayed A.-M. Osman
- Laboratory of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
- Department of Genetics, Faculty of Agriculture, Minia University, El Minia, Eg-61517, Egypt
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan
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Hata A, Nunome M, Suwanasopee T, Duengkae P, Chaiwatana S, Chamchumroon W, Suzuki T, Koonawootrittriron S, Matsuda Y, Srikulnath K. 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. [PMID: 33479400 PMCID: PMC7820500 DOI: 10.1038/s41598-021-81589-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023] Open
Abstract
In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.
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Affiliation(s)
- Ayano Hata
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Soontorn Chaiwatana
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Wiyada Chamchumroon
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Takayuki Suzuki
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Yoichi Matsuda
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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