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      Indications for Three Independent Domestication Events for the Tea Plant ( Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

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          Abstract

          Background

          Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant ( Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking.

          Methodology/Principal Findings

          Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type.

          Conclusions

          We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs.

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          Most cited references17

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          A single domestication for maize shown by multilocus microsatellite genotyping.

          There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.
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            The nature of selection during plant domestication.

            Plant domestication is an outstanding example of plant-animal co-evolution and is a far richer model for studying evolution than is generally appreciated. There have been numerous studies to identify genes associated with domestication, and archaeological work has provided a clear understanding of the dynamics of human cultivation practices during the Neolithic period. Together, these have provided a better understanding of the selective pressures that accompany crop domestication, and they demonstrate that a synthesis from the twin vantage points of genetics and archaeology can expand our understanding of the nature of evolutionary selection that accompanies domestication.
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              Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops.

              Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied 'model' crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                24 May 2016
                2016
                : 11
                : 5
                : e0155369
                Affiliations
                [1 ]Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
                [2 ]Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
                [3 ]University of Chinese Academy of Science, Beijing 10049, China
                [4 ]Coconut Research Institute, Lunuwila, Sri Lanka
                [5 ]World Agroforestry Centre, Nairobi, Kenya
                [6 ]Department of Botany, Dinhata College, Dinhata– 736135, West Bengal, India
                [7 ]Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, United Kingdom
                [8 ]Centre for Mountain Ecosystem Studies and World Agroforestry Centre East and Central Asia Regional Office, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
                [9 ]Tea Research Institute of Yunnan Academy of Agricultural Sciences, Menghai 666201, China
                Washington University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: LMG DZL. Performed the experiments: MKM MCW MML. Analyzed the data: MKM MCW MML. Contributed reagents/materials/analysis tools: LMG DZL KKT JBY JCX BYL SR JL. Wrote the paper: MKM LMG MM.

                Article
                PONE-D-15-47079
                10.1371/journal.pone.0155369
                4878758
                27218820
                f15120c9-8add-4b45-aa3e-1431fa8e9e3c
                © 2016 Meegahakumbura et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 15 November 2015
                : 27 April 2016
                Page count
                Figures: 3, Tables: 3, Pages: 14
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31161140350
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002855, Ministry of Science and Technology of the People's Republic of China;
                Award ID: 2012FY110800
                Award Recipient :
                Funded by: Applied Fundamental Research Foundation of Yunnan Province
                Award ID: 2014GA003
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31160175
                Award Recipient :
                This work was funded by the National Natural Science Foundation of China (grant number: 31161140350 to LMG, grant number: 31160175 to BYL, http://www.nsfc.gov.cn), the Ministry of Science and Technology of the People's Republic of China (grant number: 2012FY110800 to LMG, http://www.most.gov.cn), and the Applied Fundamental Research Foundation of Yunnan Province (grant number: 2014GA003 to DZL, http://www.ynstc.gov.cn). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Nutrition
                Diet
                Beverages
                Tea
                Medicine and Health Sciences
                Nutrition
                Diet
                Beverages
                Tea
                People and Places
                Geographical Locations
                Asia
                China
                People and Places
                Geographical Locations
                Asia
                India
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Mutant Genotypes
                Biology and Life Sciences
                Genetics
                Heredity
                Heterozygosity
                Biology and Life Sciences
                Organisms
                Animals
                Animal Types
                Domestic Animals
                Biology and Life Sciences
                Zoology
                Animal Types
                Domestic Animals
                Biology and Life Sciences
                Genetics
                Plant Genetics
                Crop Genetics
                Biology and Life Sciences
                Plant Science
                Plant Genetics
                Crop Genetics
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Genetics
                Population Genetics
                Phylogeography
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Custom metadata
                Microsatellite Data sets have been deposited in the Dryad Digital Repository under the doi: 10.5061/dryad.6gq1g.

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