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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 30 of 30

  1. Content type: Research article

    Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experimen...

    Authors: Shiaoman Chao, Jorge Dubcovsky, Jan Dvorak, Ming-Cheng Luo, Stephen P Baenziger, Rustam Matnyazov, Dale R Clark, Luther E Talbert, James A Anderson, Susanne Dreisigacker, Karl Glover, Jianli Chen, Kim Campbell, Phil L Bruckner, Jackie C Rudd, Scott Haley…

    Citation: BMC Genomics 2010 11:727

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  2. Content type: Research article

    The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism und...

    Authors: Zhangying Wang, Boping Fang, Jingyi Chen, Xiongjian Zhang, Zhongxia Luo, Lifei Huang, Xinliang Chen and Yujun Li

    Citation: BMC Genomics 2010 11:726

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  3. Content type: Research article

    Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic a...

    Authors: Haiyuan Yang, Liwei Hu, Thomas Hurek and Barbara Reinhold-Hurek

    Citation: BMC Genomics 2010 11:705

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  4. Content type: Research article

    A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their res...

    Authors: Eduard D Akhunov, Alina R Akhunova, Olin D Anderson, James A Anderson, Nancy Blake, Michael T Clegg, Devin Coleman-Derr, Emily J Conley, Curt C Crossman, Karin R Deal, Jorge Dubcovsky, Bikram S Gill, Yong Q Gu, Jakub Hadam, Hwayoung Heo, Naxin Huo…

    Citation: BMC Genomics 2010 11:702

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  5. Content type: Methodology article

    A five-dimensional (5-D) clone pooling strategy for screening of bacterial artificial chromosome (BAC) clones with molecular markers utilizing highly-parallel Illumina GoldenGate assays and PCR facilitates hig...

    Authors: Frank M You, Ming-Cheng Luo, Kenong Xu, Karin R Deal, Olin D Anderson and Jan Dvorak

    Citation: BMC Genomics 2010 11:692

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  6. Content type: Research article

    Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fr...

    Authors: Meghan M Mensack, Vanessa K Fitzgerald, Elizabeth P Ryan, Matthew R Lewis, Henry J Thompson and Mark A Brick

    Citation: BMC Genomics 2010 11:686

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  7. Content type: Research article

    Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because E...

    Authors: Hiroshi Mizuno, Yoshihiro Kawahara, Hiroaki Sakai, Hiroyuki Kanamori, Hironobu Wakimoto, Harumi Yamagata, Youko Oono, Jianzhong Wu, Hiroshi Ikawa, Takeshi Itoh and Takashi Matsumoto

    Citation: BMC Genomics 2010 11:683

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  8. Content type: Research article

    De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produ...

    Authors: Eshchar Mizrachi, Charles A Hefer, Martin Ranik, Fourie Joubert and Alexander A Myburg

    Citation: BMC Genomics 2010 11:681

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  9. Content type: Research article

    Riverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological compo...

    Authors: Olga Pechanova, Chuan-Yu Hsu, Joshua P Adams, Tibor Pechan, Lindsay Vandervelde, Jenny Drnevich, Sara Jawdy, Ardeshir Adeli, Jeffrey C Suttle, Amanda M Lawrence, Timothy J Tschaplinski, Armand Séguin and Cetin Yuceer

    Citation: BMC Genomics 2010 11:674

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  10. Content type: Research article

    Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitutio...

    Authors: Jianjun Xu, Qiang Zhao, Peina Du, Chenwu Xu, Baohe Wang, Qi Feng, Qiaoquan Liu, Shuzhu Tang, Minghong Gu, Bin Han and Guohua Liang

    Citation: BMC Genomics 2010 11:656

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  11. Content type: Research article

    Advanced cycle breeding utilizes crosses among elite lines and is a successful method to develop new inbreds. However, it results in a reduction in genetic diversity within the breeding population. The develop...

    Authors: María Muñoz-Amatriaín, Yanwen Xiong, Mark R Schmitt, Hatice Bilgic, Allen D Budde, Shiaoman Chao, Kevin P Smith and Gary J Muehlbauer

    Citation: BMC Genomics 2010 11:653

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  12. Content type: Research article

    The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, ...

    Authors: Saneyoshi Ueno, Grégoire Le Provost, Valérie Léger, Christophe Klopp, Céline Noirot, Jean-Marc Frigerio, Franck Salin, Jérôme Salse, Michael Abrouk, Florent Murat, Oliver Brendel, Jérémy Derory, Pierre Abadie, Patrick Léger, Cyril Cabane, Aurélien Barré…

    Citation: BMC Genomics 2010 11:650

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  13. Content type: Research article

    Widespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of pai...

    Authors: Sonali Dubey, Prashant Misra, Sanjay Dwivedi, Sandipan Chatterjee, Sumit K Bag, Shrikant Mantri, Mehar H Asif, Arti Rai, Smita Kumar, Manju Shri, Preeti Tripathi, Rudra D Tripathi, Prabodh K Trivedi, Debasis Chakrabarty and Rakesh Tuli

    Citation: BMC Genomics 2010 11:648

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  14. Content type: Research article

    The EcoTILLING technique allows polymorphisms in target genes of natural populations to be quickly analysed or identified and facilitates the screening of genebank collections for desired traits. We have devel...

    Authors: Vicente P Ibiza, Joaquín Cañizares and Fernando Nuez

    Citation: BMC Genomics 2010 11:631

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  15. Content type: Research article

    Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-i...

    Authors: David Cohen, Marie-Béatrice Bogeat-Triboulot, Emilie Tisserant, Sandrine Balzergue, Marie-Laure Martin-Magniette, Gaëlle Lelandais, Nathalie Ningre, Jean-Pierre Renou, Jean-Philippe Tamby, Didier Le Thiec and Irène Hummel

    Citation: BMC Genomics 2010 11:630

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  16. Content type: Research article

    The barley-Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative tr...

    Authors: Xinwei Chen, Rients E Niks, Peter E Hedley, Jenny Morris, Arnis Druka, Thierry C Marcel, Anton Vels and Robbie Waugh

    Citation: BMC Genomics 2010 11:629

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  17. Content type: Research article

    The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relativel...

    Authors: Guang-Chen Fang, Barbara P Blackmon, David C Henry, Margaret E Staton, Christopher A Saski, Scott A Hodges, Jeff P Tomkins and Hong Luo

    Citation: BMC Genomics 2010 11:621

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  18. Content type: Research article

    Although melon (Cucumis melo L.) is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,02...

    Authors: Víctor M González, Luis Rodríguez-Moreno, Emilio Centeno, Andrej Benjak, Jordi Garcia-Mas, Pere Puigdomènech and Miguel A Aranda

    Citation: BMC Genomics 2010 11:618

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  19. Content type: Research article

    Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as...

    Authors: Purushothaman Natarajan, Deepa Kanagasabapathy, Gnanasekaran Gunadayalan, Jasintha Panchalingam, Noopur shree, Priyanka Annabel Sugantham, Kavita Kumari Singh and Parani Madasamy

    Citation: BMC Genomics 2010 11:606

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  20. Content type: Research article

    Sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpota...

    Authors: Roland Schafleitner, Luz R Tincopa, Omar Palomino, Genoveva Rossel, Ronald F Robles, Rocio Alagon, Carlos Rivera, Cynthia Quispe, Luis Rojas, Jaime A Pacheco, Julio Solis, Diogenes Cerna, Ji Young Kim, Jack Hou and Reinhard Simon

    Citation: BMC Genomics 2010 11:604

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  21. Content type: Research article

    Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea t...

    Authors: Ludmila Tyler, Jennifer N Bragg, Jiajie Wu, Xiaohan Yang, Gerald A Tuskan and John P Vogel

    Citation: BMC Genomics 2010 11:600

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  22. Content type: Research article

    Many plant species have been investigated in the last years for the identification and characterization of the corresponding miRNAs, nevertheless extensive studies are not yet available on barley (at the time ...

    Authors: Moreno Colaiacovo, Annalisa Subacchi, Paolo Bagnaresi, Antonella Lamontanara, Luigi Cattivelli and Primetta Faccioli

    Citation: BMC Genomics 2010 11:595

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  23. Content type: Research article

    The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassi...

    Authors: Jinsong Xu, Xiaoju Qian, Xiaofeng Wang, Ruiyuan Li, Xiaomao Cheng, Yuan Yang, Jie Fu, Shunchang Zhang, Graham J King, Jiangsheng Wu and Kede Liu

    Citation: BMC Genomics 2010 11:594

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  24. Content type: Research article

    Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellu...

    Authors: Stéphane Fenart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins and Brigitte Thomasset

    Citation: BMC Genomics 2010 11:592

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  25. Content type: Research article

    Flavonoid 3',5'-hydroxylases (F3'5'Hs) and flavonoid 3'-hydroxylases (F3'Hs) competitively control the synthesis of delphinidin and cyanidin, the precursors of blue and red anthocyanins. In most plants, F3'5'H ge...

    Authors: Luigi Falginella, Simone D Castellarin, Raffaele Testolin, Gregory A Gambetta, Michele Morgante and Gabriele Di Gaspero

    Citation: BMC Genomics 2010 11:562

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  26. Content type: Research article

    Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent...

    Authors: Iraj Tavassolian, Gholmereza Rabiei, Davina Gregory, Mourad Mnejja, Michelle G Wirthensohn, Peter W Hunt, John P Gibson, Christopher M Ford, Margaret Sedgley and Shu-Biao Wu

    Citation: BMC Genomics 2010 11:551

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  27. Content type: Research article

    Plant class III peroxidases exist as a large multigenic family involved in numerous functions suggesting a functional specialization of each gene. However, few genes have been linked with a specific function. ...

    Authors: Claudia Cosio and Christophe Dunand

    Citation: BMC Genomics 2010 11:528

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