Identification of Pummelo Cultivars by Using a Panel of 25 Selected SNPs and 12 DNA Segments
Identifieur interne : 000A49 ( Main/Exploration ); précédent : 000A48; suivant : 000A50Identification 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
Affiliations:
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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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></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="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></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><wicri:noRegion>Yunnan</wicri:noRegion></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><wicri:noRegion>Chongqing</wicri:noRegion></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><wicri:noRegion>Chongqing</wicri:noRegion></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="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhong, Yun" sort="Zhong, Yun" uniqKey="Zhong Y" first="Yun" last="Zhong">Yun Zhong</name><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></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><wicri:noRegion>Chongqing</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Bo" sort="Jiang, Bo" uniqKey="Jiang B" first="Bo" last="Jiang">Bo Jiang</name><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></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="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhang, Li" sort="Zhang, Li" uniqKey="Zhang L" first="Li" last="Zhang">Li Zhang</name><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="3"><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><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></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><wicri:noRegion>Chongqing</wicri:noRegion></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><wicri:noRegion>Chongqing</wicri:noRegion></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><wicri:noRegion>Yunnan</wicri:noRegion></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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Bremer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Distefano, G" uniqKey="Distefano G">G Distefano</name></author><author><name sortKey="Caruso, M" uniqKey="Caruso M">M Caruso</name></author><author><name sortKey="La Malfa, S" uniqKey="La Malfa S">S La Malfa</name></author><author><name sortKey="Gentile, A" uniqKey="Gentile A">A Gentile</name></author><author><name sortKey="Wu, Sb" uniqKey="Wu S">SB Wu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Distefano, G" uniqKey="Distefano G">G Distefano</name></author><author><name sortKey="La Malfa, S" uniqKey="La Malfa S">S La Malfa</name></author><author><name sortKey="Gentile, A" uniqKey="Gentile A">A Gentile</name></author><author><name sortKey="Wu, Sb" uniqKey="Wu S">SB Wu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bret, Mp" uniqKey="Bret M">MP Bretó</name></author><author><name sortKey="Ruiz, C" uniqKey="Ruiz C">C Ruiz</name></author><author><name sortKey="Pina J, A" uniqKey="Pina J A">a Pina J</name></author><author><name sortKey="Asins, Mj" uniqKey="Asins M">MJ Asíns</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Corazza Nunes, Mj" uniqKey="Corazza Nunes M">MJ Corazza-Nunes</name></author><author><name sortKey="Machado, Ma" uniqKey="Machado M">MA Machado</name></author><author><name sortKey="Nunes, Wmc" uniqKey="Nunes W">WMC Nunes</name></author><author><name sortKey="Cristofani, M" uniqKey="Cristofani M">M Cristofani</name></author><author><name sortKey="Targon, Mlpn" uniqKey="Targon M">MLPN Targon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hodgson, Rw" uniqKey="Hodgson R">RW Hodgson</name></author><author><name sortKey="Reuther, W" uniqKey="Reuther W">W Reuther</name></author><author><name sortKey="Webber, Hj" uniqKey="Webber H">HJ Webber</name></author><author><name sortKey="Batchelor, Ld" uniqKey="Batchelor L">LD 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><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Guangdong</li></region><settlement><li>Jiangmen</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wu, Bo" sort="Wu, Bo" uniqKey="Wu B" first="Bo" last="Wu">Bo Wu</name></noRegion><name sortKey="Bei, Xue Jun" sort="Bei, Xue Jun" uniqKey="Bei X" first="Xue-Jun" last="Bei">Xue-Jun Bei</name><name sortKey="Jiang, Bo" sort="Jiang, Bo" uniqKey="Jiang B" first="Bo" last="Jiang">Bo Jiang</name><name sortKey="Jiang, Bo" sort="Jiang, Bo" uniqKey="Jiang B" first="Bo" last="Jiang">Bo Jiang</name><name sortKey="Li, Chong" sort="Li, Chong" uniqKey="Li C" first="Chong" last="Li">Chong Li</name><name sortKey="Li, Yue Jia" sort="Li, Yue Jia" uniqKey="Li Y" first="Yue-Jia" last="Li">Yue-Jia Li</name><name sortKey="Li, Yue Jia" sort="Li, Yue Jia" uniqKey="Li Y" first="Yue-Jia" last="Li">Yue-Jia Li</name><name sortKey="Wang, Xuan" sort="Wang, Xuan" uniqKey="Wang X" first="Xuan" last="Wang">Xuan Wang</name><name sortKey="Wu, Bo" sort="Wu, Bo" uniqKey="Wu B" first="Bo" last="Wu">Bo Wu</name><name sortKey="Wu, Bo" sort="Wu, Bo" uniqKey="Wu B" first="Bo" last="Wu">Bo Wu</name><name sortKey="Yan, Shu Tang" sort="Yan, Shu Tang" uniqKey="Yan S" first="Shu-Tang" last="Yan">Shu-Tang Yan</name><name sortKey="Yang, Run Ting" sort="Yang, Run Ting" uniqKey="Yang R" first="Run-Ting" last="Yang">Run-Ting Yang</name><name sortKey="Yue, Jian Qiang" sort="Yue, Jian Qiang" uniqKey="Yue J" first="Jian-Qiang" last="Yue">Jian-Qiang Yue</name><name sortKey="Zeng, Ji Wu" sort="Zeng, Ji Wu" uniqKey="Zeng J" first="Ji-Wu" last="Zeng">Ji-Wu Zeng</name><name sortKey="Zeng, Ji Wu" sort="Zeng, Ji Wu" uniqKey="Zeng J" first="Ji-Wu" last="Zeng">Ji-Wu Zeng</name><name sortKey="Zhang, Li" sort="Zhang, Li" uniqKey="Zhang L" first="Li" last="Zhang">Li Zhang</name><name sortKey="Zhang, Li" sort="Zhang, Li" uniqKey="Zhang L" first="Li" last="Zhang">Li Zhang</name><name sortKey="Zhong, Guang Yan" sort="Zhong, Guang Yan" uniqKey="Zhong G" first="Guang-Yan" last="Zhong">Guang-Yan Zhong</name><name sortKey="Zhong, Yun" sort="Zhong, Yun" uniqKey="Zhong Y" first="Yun" last="Zhong">Yun Zhong</name><name sortKey="Zhong, Yun" sort="Zhong, Yun" uniqKey="Zhong Y" first="Yun" last="Zhong">Yun Zhong</name><name sortKey="Zhou, Dong Guo" sort="Zhou, Dong Guo" uniqKey="Zhou D" first="Dong-Guo" last="Zhou">Dong-Guo Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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