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      Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

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          Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP), Chinese white pear (CWP), Chinese sand pear (CSP), and Ussurian pear (UP), but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR) markers and two non-coding chloroplast DNA (cpDNA) regions ( trnL- trnF and accD- psaI). High levels of genetic diversity were detected for both nSSRs ( H E = 0.744) and cpDNAs ( Hd = 0.792). The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a) JPs; (b) cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c) cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be originated from the interspecific hybridization of wild Pyrus ussuriensis with cultivated Pyrus pyrifolia. The combination of uniparental DNA sequences and nuclear markers give us a better understanding of origins and genetic relationships for Asian pear groups and will be beneficial for the future improvement of Asian pear cultivars.

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          Most cited references 62

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          The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
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                Author and article information

                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                07 May 2018
                : 9
                1Department of Horticulture, Zhejiang University , Hangzhou, China
                2The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China , Hangzhou, China
                3Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants , Hangzhou, China
                4College of Ecology, Lishui University , Lishui, China
                5College of Agriculture, Guizhou University , Guiyang, China
                6Research Institute of Pomology, Chinese Academy of Agricultural Sciences , Xingcheng, China
                7Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences , Wuhan, China
                Author notes

                Edited by: Rosane Garcia Collevatti, Universidade Federal de Goiás, Brazil

                Reviewed by: Rosana Vianello, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Brazil; Hovirag Lancioni, University of Perugia, Italy

                *Correspondence: Yuanwen Teng, ywteng@

                These authors have contributed equally to this work.

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

                Copyright © 2018 Yue, Zheng, Zong, Jiang, Hu, Yu, Liu, Cao, Hu and Teng.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Figures: 4, Tables: 2, Equations: 0, References: 77, Pages: 16, Words: 0
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 30871690
                Plant Science
                Original Research


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