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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 29 of 30

  1. Content type: Research article

    Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly ...

    Authors: Jean-Marc Gion, Audrey Carouché, Sylvie Deweer, Franck Bedon, Frédérique Pichavant, Jean-Paul Charpentier, Henri Baillères, Philippe Rozenberg, Victor Carocha, Nina Ognouabi, Daniel Verhaegen, Jacqueline Grima-Pettenati, Philippe Vigneron and Christophe Plomion

    Citation: BMC Genomics 2011 12:301

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  2. Content type: Research article

    To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes r...

    Authors: Debbie Laudencia-Chingcuanco, Seedhabadee Ganeshan, Frank You, Brian Fowler, Ravindra Chibbar and Olin Anderson

    Citation: BMC Genomics 2011 12:299

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  3. Content type: Research article

    One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to...

    Authors: Patricia Faivre Rampant, Isabelle Lesur, Clément Boussardon, Frédérique Bitton, Marie-Laure Martin-Magniette, Catherine Bodénès, Grégoire Le Provost, Hélène Bergès, Sylvia Fluch, Antoine Kremer and Christophe Plomion

    Citation: BMC Genomics 2011 12:292

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  4. Content type: Research article

    Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific impo...

    Authors: Lu Wang, Xiang Yu, Han Wang, Yi-Zhen Lu, Marjo de Ruiter, Marcel Prins and Yu-Ke He

    Citation: BMC Genomics 2011 12:289

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  5. Content type: Software

    The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping ...

    Authors: Jose M Blanca, Laura Pascual, Peio Ziarsolo, Fernando Nuez and Joaquin Cañizares

    Citation: BMC Genomics 2011 12:285

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  6. Content type: Research article

    Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to dr...

    Authors: Sota Fujii, Takushi Toda, Shunsuke Kikuchi, Ryutaro Suzuki, Koji Yokoyama, Hiroko Tsuchida, Kentaro Yano and Kinya Toriyama

    Citation: BMC Genomics 2011 12:279

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  7. Content type: Research article

    A deficiency in phaseolin and phytohemagglutinin is associated with a near doubling of sulfur amino acid content in genetically related lines of common bean (Phaseolus vulgaris), particularly cysteine, elevated b...

    Authors: Fuqiang Yin, Agnieszka Pajak, Ralph Chapman, Andrew Sharpe, Shangzhi Huang and Frédéric Marsolais

    Citation: BMC Genomics 2011 12:268

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  8. Content type: Research article

    Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to oth...

    Authors: Sukhjiwan Kaur, Noel OI Cogan, Luke W Pembleton, Maiko Shinozuka, Keith W Savin, Michael Materne and John W Forster

    Citation: BMC Genomics 2011 12:265

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  9. Content type: Research article

    Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene ex...

    Authors: W Walter Lorenz, Rob Alba, Yuan-Sheng Yu, John M Bordeaux, Marta Simões and Jeffrey FD Dean

    Citation: BMC Genomics 2011 12:264

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  10. Content type: Methodology article

    Phenotype-driven forward genetic experiments are powerful approaches for linking phenotypes to genomic elements but they still involve a laborious positional cloning process. Although sequencing of complete ge...

    Authors: Michal Mokry, Isaäc J Nijman, Anja van Dijken, Rene Benjamins, Renze Heidstra, Ben Scheres and Edwin Cuppen

    Citation: BMC Genomics 2011 12:256

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  11. Content type: Research article

    Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model...

    Authors: Christian Clepet, Tarek Joobeur, Yi Zheng, Delphine Jublot, Mingyun Huang, Veronica Truniger, Adnane Boualem, Maria Elena Hernandez-Gonzalez, Ramon Dolcet-Sanjuan, Vitaly Portnoy, Albert Mascarell-Creus, Ana I Caño-Delgado, Nurit Katzir, Abdelhafid Bendahmane, James J Giovannoni, Miguel A Aranda…

    Citation: BMC Genomics 2011 12:252

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  12. Content type: Research article

    Sequence related amplified polymorphism (SRAP) is commonly used to construct high density genetic maps, map genes and QTL of important agronomic traits in crops and perform genetic diversity analysis without k...

    Authors: Wei Li, Jiefu Zhang, Yanglong Mou, Jianfeng Geng, Peter BE McVetty, Shengwu Hu and Genyi Li

    Citation: BMC Genomics 2011 12:249

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  13. Content type: Research article

    Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic gen...

    Authors: Daniela Schulte, Ruvini Ariyadasa, Bujun Shi, Delphine Fleury, Chris Saski, Michael Atkins, Pieter deJong, Cheng-Cang Wu, Andreas Graner, Peter Langridge and Nils Stein

    Citation: BMC Genomics 2011 12:247

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  14. Content type: Research article

    Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising...

    Authors: Kazuhiro Sato, Yuka Motoi, Nami Yamaji and Hideya Yoshida

    Citation: BMC Genomics 2011 12:246

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  15. Content type: Research article

    Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was l...

    Authors: Yan Wang, Silong Sun, Bo Liu, Hui Wang, Jie Deng, Yongcui Liao, Qian Wang, Feng Cheng, Xiaowu Wang and Jian Wu

    Citation: BMC Genomics 2011 12:239

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  16. Content type: Research article

    Resistance of soybean (Glycine max L. Merr.) cultivars to populations of cyst nematode (SCN; Heterodera glycines I.) was complicated by the diversity of HG Types (biotypes), the multigenic nature of resistance an...

    Authors: Wei Chang, Limin Dong, Zizhen Wang, Haibo Hu, Yingpeng Han, Weili Teng, Hongxia Zhang, Maozu Guo and Wenbin Li

    Citation: BMC Genomics 2011 12:233

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  17. Content type: Research article

    The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic res...

    Authors: Susanne U Franssen, Roshan P Shrestha, Andrea Bräutigam, Erich Bornberg-Bauer and Andreas PM Weber

    Citation: BMC Genomics 2011 12:227

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  18. Content type: Research article

    Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root...

    Authors: Heba MM Ibrahim, Parsa Hosseini, Nadim W Alkharouf, Ebtissam HA Hussein, Abd El Kader Y Gamal El-Din, Mohammed AM Aly and Benjamin F Matthews

    Citation: BMC Genomics 2011 12:220

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  19. Content type: Research article

    Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are asso...

    Authors: Raja Ragupathy, Rajkumar Rathinavelu and Sylvie Cloutier

    Citation: BMC Genomics 2011 12:217

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  20. Content type: Research article

    In the presence of drought and other desiccating stresses, plants synthesize and redistribute the phytohormone abscisic acid (ABA). ABA promotes plant water conservation by acting on specialized cells in the l...

    Authors: Rui-Sheng Wang, Sona Pandey, Song Li, Timothy E Gookin, Zhixin Zhao, Réka Albert and Sarah M Assmann

    Citation: BMC Genomics 2011 12:216

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  21. Content type: Research article

    Due to its overarching role in genome function, sequence-dependent DNA curvature continues to attract great attention. The DNA double helix is not a rigid cylinder, but presents both curvature and flexibility ...

    Authors: Ali Masoudi-Nejad, Sara Movahedi and Ruy Jáuregui

    Citation: BMC Genomics 2011 12:214

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  22. Content type: Research article

    Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. Thi...

    Authors: Shannon CK Straub, Mark Fishbein, Tatyana Livshultz, Zachary Foster, Matthew Parks, Kevin Weitemier, Richard C Cronn and Aaron Liston

    Citation: BMC Genomics 2011 12:211

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  23. Content type: Research article

    Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infa...

    Authors: S Samuel Yang, Zheng Jin Tu, Foo Cheung, Wayne Wenzhong Xu, JoAnn FS Lamb, Hans-Joachim G Jung, Carroll P Vance and John W Gronwald

    Citation: BMC Genomics 2011 12:199

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  24. Content type: Research article

    Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit it...

    Authors: Purushothaman Natarajan and Madasamy Parani

    Citation: BMC Genomics 2011 12:191

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  25. Content type: Research article

    Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both ...

    Authors: R C Venu, M V Sreerekha, Kan Nobuta, André Beló, Yuese Ning, Gynheung An, Blake C Meyers and Guo-Liang Wang

    Citation: BMC Genomics 2011 12:190

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  26. Content type: Research article

    Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate ...

    Authors: Leandro G Neves, Eva MC Mamani, Acelino C Alfenas, Matias Kirst and Dario Grattapaglia

    Citation: BMC Genomics 2011 12:189

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  27. Content type: Research article

    Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongatio...

    Authors: Hongyan Xing, Ramesh N Pudake, Ganggang Guo, Guofang Xing, Zhaorong Hu, Yirong Zhang, Qixin Sun and Zhongfu Ni

    Citation: BMC Genomics 2011 12:178

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  28. Content type: Database

    The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-thro...

    Authors: Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jingchu Luo and Ge Gao

    Citation: BMC Genomics 2011 12:165

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  29. Content type: Research article

    Plant mitochondria, semiautonomous organelles that function as manufacturers of cellular ATP, have their own genome that has a slow rate of evolution and rapid rearrangement. Cytoplasmic male sterility (CMS), ...

    Authors: Huitao Liu, Peng Cui, Kehui Zhan, Qiang Lin, Guoyin Zhuo, Xiaoli Guo, Feng Ding, Wenlong Yang, Dongcheng Liu, Songnian Hu, Jun Yu and Aimin Zhang

    Citation: BMC Genomics 2011 12:163

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  30. Content type: Research article

    Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molec...

    Authors: Di Wang, Yajiao Pan, Xiuqin Zhao, Linghua Zhu, Binying Fu and Zhikang Li

    Citation: BMC Genomics 2011 12:149

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  31. Content type: Research article

    The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be ...

    Authors: Betty Pelgas, Jean Bousquet, Patrick G Meirmans, Kermit Ritland and Nathalie Isabel

    Citation: BMC Genomics 2011 12:145

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  32. Content type: Research article

    Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding pr...

    Authors: Jorge AP Paiva, Elisa Prat, Sonia Vautrin, Mauro D Santos, Hélène San-Clemente, Sérgio Brommonschenkel, Paulo GS Fonseca, Dario Grattapaglia, Xiang Song, Jetty SS Ammiraju, David Kudrna, Rod A Wing, Ana T Freitas, Hélène Bergès and Jacqueline Grima-Pettenati

    Citation: BMC Genomics 2011 12:137

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  33. Content type: Research article

    Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little genomic inform...

    Authors: Cheng-Ying Shi, Hua Yang, Chao-Ling Wei, Oliver Yu, Zheng-Zhu Zhang, Chang-Jun Jiang, Jun Sun, Ye-Yun Li, Qi Chen, Tao Xia and Xiao-Chun Wan

    Citation: BMC Genomics 2011 12:131

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  34. Content type: Research article

    MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced g...

    Authors: Andreas W Schreiber, Bu-Jun Shi, Chun-Yuan Huang, Peter Langridge and Ute Baumann

    Citation: BMC Genomics 2011 12:129

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  35. Content type: Research article

    Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by inf...

    Authors: Sara Sestili, Annalisa Polverari, Laura Luongo, Alberto Ferrarini, Michele Scotton, Jamshaid Hussain, Massimo Delledonne, Nadia Ficcadenti and Alessandra Belisario

    Citation: BMC Genomics 2011 12:122

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  36. Content type: Research article

    Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the lo...

    Authors: Rashmi Gaur, Niroj K Sethy, Shalu Choudhary, Bhumika Shokeen, Varsha Gupta and Sabhyata Bhatia

    Citation: BMC Genomics 2011 12:117

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  37. Content type: Database

    DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid...

    Authors: Daniel Baron, Emeric Dubois, Audrey Bihouée, Raluca Teusan, Marja Steenman, Philippe Jourdon, Armelle Magot, Yann Péréon, Reiner Veitia, Frédérique Savagner, Gérard Ramstein and Rémi Houlgatte

    Citation: BMC Genomics 2011 12:113

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  38. Content type: Methodology article

    Several tools are available to identify miRNAs from deep-sequencing data, however, only a few of them, like miRDeep, can identify novel miRNAs and are also available as a standalone application. Given the diff...

    Authors: Vivek Thakur, Samart Wanchana, Mercedes Xu, Richard Bruskiewich, William Paul Quick, Axel Mosig and Xin-Guang Zhu

    Citation: BMC Genomics 2011 12:108

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  39. Content type: Research article

    Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat ...

    Authors: José Blanca, Joaquín Cañizares, Cristina Roig, Pello Ziarsolo, Fernando Nuez and Belén Picó

    Citation: BMC Genomics 2011 12:104

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  40. Content type: Research article

    The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing map...

    Authors: Jun Wang, Derek J Lydiate, Isobel AP Parkin, Cyril Falentin, Régine Delourme, Pierre WC Carion and Graham J King

    Citation: BMC Genomics 2011 12:101

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  41. Content type: Research article

    Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular ...

    Authors: Satya S Narina, Ramesh Buyyarapu, Kameswara Rao Kottapalli, Alieu M Sartie, Mohamed I Ali, Asiedu Robert, Mignouna JD Hodeba, Brian L Sayre and Brian E Scheffler

    Citation: BMC Genomics 2011 12:100

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  42. Content type: Research article

    Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in f...

    Authors: Joshua P Der, Michael S Barker, Norman J Wickett, Claude W dePamphilis and Paul G Wolf

    Citation: BMC Genomics 2011 12:99

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  43. Content type: Research article

    Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence ...

    Authors: Rebekah E Oliver, Gerard R Lazo, Joseph D Lutz, Marc J Rubenfield, Nicholas A Tinker, Joseph M Anderson, Nicole H Wisniewski Morehead, Dinesh Adhikary, Eric N Jellen, P Jeffrey Maughan, Gina L Brown Guedira, Shiaoman Chao, Aaron D Beattie, Martin L Carson, Howard W Rines, Donald E Obert…

    Citation: BMC Genomics 2011 12:77

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  44. Content type: Research article

    Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the H...

    Authors: Yong-Xiang Lin, Hai-Yang Jiang, Zhang-Xin Chu, Xiu-Li Tang, Su-Wen Zhu and Bei-Jiu Cheng

    Citation: BMC Genomics 2011 12:76

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  45. Content type: Research article

    After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that ...

    Authors: Jin-Zhi Zhang, Xiao-Yan Ai, Lei-Ming Sun, Dong-Liang Zhang, Wen-Wu Guo, Xiu-Xin Deng and Chun-Gen Hu

    Citation: BMC Genomics 2011 12:63

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