Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments
Identifieur interne : 001198 ( Pmc/Curation ); précédent : 001197; suivant : 001199Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments
Auteurs : Bo Wu [République populaire de Chine] ; Guang-Yan Zhong [République populaire de Chine] ; Jian-Qiang Yue [République populaire de Chine] ; Run-Ting Yang [République populaire de Chine] ; Chong Li [République populaire de Chine] ; Yue-Jia Li [République populaire de Chine] ; Yun Zhong [République populaire de Chine] ; Xuan Wang [République populaire de Chine] ; Bo Jiang [République populaire de Chine] ; Ji-Wu Zeng [République populaire de Chine] ; Li Zhang [République populaire de Chine] ; Shu-Tang Yan [République populaire de Chine] ; Xue-Jun Bei [République populaire de Chine] ; Dong-Guo Zhou [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.
Url:
DOI: 10.1371/journal.pone.0094506
PubMed: 24732455
PubMed Central: 3986212
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Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Bei, Xue Jun" sort="Bei, Xue Jun" uniqKey="Bei X" first="Xue-Jun" last="Bei">Xue-Jun Bei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Zhou, Dong Guo" sort="Zhou, Dong Guo" uniqKey="Zhou D" first="Dong-Guo" last="Zhou">Dong-Guo Zhou</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24732455</idno><idno type="pmc">3986212</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986212</idno><idno type="RBID">PMC:3986212</idno><idno type="doi">10.1371/journal.pone.0094506</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001199</idno><idno type="wicri:Area/Pmc/Curation">001198</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments</title><author><name sortKey="Wu, Bo" sort="Wu, Bo" uniqKey="Wu B" first="Bo" last="Wu">Bo Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Zhong, Guang Yan" sort="Zhong, Guang Yan" uniqKey="Zhong G" first="Guang-Yan" last="Zhong">Guang-Yan Zhong</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Yue, Jian Qiang" sort="Yue, Jian Qiang" uniqKey="Yue J" first="Jian-Qiang" last="Yue">Jian-Qiang Yue</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Yang, Run Ting" sort="Yang, Run Ting" uniqKey="Yang R" first="Run-Ting" last="Yang">Run-Ting Yang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Li, Chong" sort="Li, Chong" uniqKey="Li C" first="Chong" last="Li">Chong Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Li, Yue Jia" sort="Li, Yue Jia" uniqKey="Li Y" first="Yue-Jia" last="Li">Yue-Jia Li</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Zhong, Yun" sort="Zhong, Yun" uniqKey="Zhong Y" first="Yun" last="Zhong">Yun Zhong</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Xuan" sort="Wang, Xuan" uniqKey="Wang X" first="Xuan" last="Wang">Xuan Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Jiang, Bo" sort="Jiang, Bo" uniqKey="Jiang B" first="Bo" last="Jiang">Bo Jiang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Zeng, Ji Wu" sort="Zeng, Ji Wu" uniqKey="Zeng J" first="Ji-Wu" last="Zeng">Ji-Wu Zeng</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Li" sort="Zhang, Li" uniqKey="Zhang L" first="Li" last="Zhang">Li Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou</wicri:regionArea></affiliation></author><author><name sortKey="Yan, Shu Tang" sort="Yan, Shu Tang" uniqKey="Yan S" first="Shu-Tang" last="Yan">Shu-Tang Yan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Bei, Xue Jun" sort="Bei, Xue Jun" uniqKey="Bei X" first="Xue-Jun" last="Bei">Xue-Jun Bei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Landscape Architecture, Southwest University, Chongqing</wicri:regionArea></affiliation></author><author><name sortKey="Zhou, Dong Guo" sort="Zhou, Dong Guo" uniqKey="Zhou D" first="Dong-Guo" last="Zhou">Dong-Guo Zhou</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chomchalow, N" uniqKey="Chomchalow N">N Chomchalow</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Ym" uniqKey="Ye Y">YM Ye</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barkley, Na" uniqKey="Barkley N">NA Barkley</name></author><author><name sortKey="Roose, Ml" uniqKey="Roose M">ML Roose</name></author><author><name sortKey="Krueger, Rr" uniqKey="Krueger R">RR Krueger</name></author><author><name sortKey="Federici, Ct" uniqKey="Federici C">CT Federici</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" 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Batchelor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tan, Wq" uniqKey="Tan W">WQ Tan</name></author><author><name sortKey="Zheng, Jl" uniqKey="Zheng J">JL Zheng</name></author><author><name sortKey="Jian, Jq" uniqKey="Jian J">JQ Jian</name></author><author><name sortKey="Diao, Jh" uniqKey="Diao J">JH Diao</name></author><author><name sortKey="Li, Sn" uniqKey="Li S">SN Li</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Gmitter, Fg" uniqKey="Gmitter F">FG Gmitter</name></author><author><name sortKey="Hu, Xl" uniqKey="Hu X">XL Hu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24732455</article-id><article-id pub-id-type="pmc">3986212</article-id><article-id pub-id-type="publisher-id">PONE-D-13-39092</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0094506</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Agriculture</subject><subj-group><subject>Crops</subject><subj-group><subject>Fruits</subject></subj-group></subj-group></subj-group><subj-group><subject>Biochemistry</subject><subj-group><subject>DNA</subject><subject>Nucleic Acids</subject></subj-group></subj-group><subj-group><subject>Biotechnology</subject></subj-group><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Population Genetics</subject><subj-group><subject>Genetic Polymorphism</subject></subj-group></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Plant Genetics</subject></subj-group></subj-group><subj-group><subject>Plant Science</subject></subj-group></subj-group></article-categories><title-group><article-title>Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments</article-title><alt-title alt-title-type="running-head">Identification of Pummelos by DNA Fingerprinting</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Bo</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhong</surname><given-names>Guang-yan</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yue</surname><given-names>Jian-qiang</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Run-ting</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Chong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Yue-jia</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhong</surname><given-names>Yun</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Xuan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Bo</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Ji-wu</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Li</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yan</surname><given-names>Shu-tang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bei</surname><given-names>Xue-jun</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Dong-guo</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Science, Dehong, Yunnan, China</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Wu</surname><given-names>Shu-Biao</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of New England, Australia</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>gy_zhong@163.com</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: GYZ BW. Performed the experiments: RTY YJL BW. Analyzed the data: BW RTY. Contributed reagents/materials/analysis tools: GYZ JQY CL YZ BJ JWZ LZ XW STY XJB DGZ. Wrote the paper: BW GYZ.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>14</day><month>4</month><year>2014</year></pub-date><volume>9</volume><issue>4</issue><elocation-id>e94506</elocation-id><history><date date-type="received"><day>23</day><month>9</month><year>2013</year></date><date date-type="accepted"><day>17</day><month>3</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Wu et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.</p></abstract><funding-group><funding-statement>This work was Supported by the International Science & Technology Cooperation Program of China (Grant No: 2012DFA30610), the National Program on Key Basic Research Project (Grant No: 2011CB100600), and the National Natural Science Foundation of China (Grant No: 30971992). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="12"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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