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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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Liang Z, Duan S, Sheng J, Zhu S, Ni X, Shao J, Liu C, Nick P, Du F, Fan P, Mao R, Zhu Y, Deng W, Yang M, Huang H, Liu Y, Ding Y, Liu X, Jiang J, Zhu Y, Li S, He X, Chen W, Dong Y. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nat Commun 2019; 10:1190. [PMID: 30867414 PMCID: PMC6416300 DOI: 10.1038/s41467-019-09135-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 02/21/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement. Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.
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Affiliation(s)
- Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Nowbio Biotechnology Company, Kunming, 650201, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuemei Ni
- BGI, BGI-Shenzhen, Shenzhen, 518120, China.,BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jianhui Shao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, 76128, Germany
| | - Fei Du
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ruzhi Mao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Weiping Deng
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yiqing Ding
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
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The complex geography of domestication of the African rice Oryza glaberrima. PLoS Genet 2019; 15:e1007414. [PMID: 30845217 PMCID: PMC6424484 DOI: 10.1371/journal.pgen.1007414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/19/2019] [Accepted: 02/08/2019] [Indexed: 11/19/2022] Open
Abstract
While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors were either mislabeled or may actually represent feral wild-domesticated hybrids. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits. For many crops it is not clear how they were domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population comparisons provide insight into the relationship between wild and cultivated populations and the evolutionary history of domestication. In this study, we investigated the domestication history of Oryza glaberrima, a rice species that was domesticated in West Africa independent from the Asian rice species O. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model for O. glaberrima—a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environments and cultivation preference of people. Hence domestication of African rice was a multi-regional process.
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Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic Insights into Date Palm Origins. Genes (Basel) 2018; 9:genes9100502. [PMID: 30336633 PMCID: PMC6211059 DOI: 10.3390/genes9100502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 11/16/2022] Open
Abstract
With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.
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Affiliation(s)
- Muriel Gros-Balthazard
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, P.O. Box 15551, Al Ain, UAE.
| | - Jonathan Mark Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA.
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Sagart L, Hsu TF, Tsai YC, Wu CC, Huang LT, Chen YC, Chen YF, Tseng YC, Lin HY, Hsing YIC. A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals. RICE (NEW YORK, N.Y.) 2018; 11:57. [PMID: 30306280 PMCID: PMC6179969 DOI: 10.1186/s12284-018-0247-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue. RESULTS We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000-5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving. CONCLUSION We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.
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Affiliation(s)
- Laurent Sagart
- Centre de Recherches Linguistiques sur l’Asie Orientale/Centre National de la Recherche Scientifique, INaLCO, 2 rue de Lille, 75007 Paris, France
| | - Tze-Fu Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, 106 Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yu-Chi Chen
- Taiwan International Cooperation and Development Fund, Taipei, 111 Taiwan
| | - Yi-Fang Chen
- Soil and Water Conservation Bureau, Council of Agriculture, Nantou, 540 Taiwan
| | - Yu-Chien Tseng
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Hung-Ying Lin
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-1085 USA
| | - Yue-ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
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Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
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