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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 26 of 30

  1. Content type: Research article

    Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little...

    Authors: Jianjun Qi, Na Zheng, Bing Zhang, Peng Sun, Songnian Hu, Wenjuan Xu, Qin Ma, Tingzhou Zhao, Lili Zhou, Mingjian Qin and Xianen Li

    Citation: BMC Genomics 2013 14:358

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  2. Content type: Research article

    Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been r...

    Authors: Nunzio D’Agostino, Tomek Golas, Henri van de Geest, Aureliano Bombarely, Thikra Dawood, Jan Zethof, Nicky Driedonks, Erik Wijnker, Joachim Bargsten, Jan-Peter Nap, Celestina Mariani and Ivo Rieu

    Citation: BMC Genomics 2013 14:356

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  3. Content type: Research article

    The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and h...

    Authors: Marcela Víquez-Zamora, Ben Vosman, Henri van de Geest, Arnaud Bovy, Richard GF Visser, Richard Finkers and Adriaan W van Heusden

    Citation: BMC Genomics 2013 14:354

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  4. Content type: Research article

    Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response...

    Authors: Wen-Chang Chi, Yun-An Chen, Yu-Chywan Hsiung, Shih-Feng Fu, Chang-Hung Chou, Ngoc Nam Trinh, Ying-Chih Chen and Hao-Jen Huang

    Citation: BMC Genomics 2013 14:351

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  5. Content type: Research article

    The presence of homoeologous sequences and absence of a reference genome sequence make discovery and genotyping of single nucleotide polymorphisms (SNPs) more challenging in polyploid crops.

    Authors: Xun Chen, Xuemin Li, Bing Zhang, Jinsong Xu, Zhikun Wu, Bo Wang, Haitao Li, Muhammad Younas, Lei Huang, Yingfeng Luo, Jiangsheng Wu, Songnian Hu and Kede Liu

    Citation: BMC Genomics 2013 14:346

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  6. Content type: Research article

    Ever since the recent completion of the peach genome, the focus of genetic research in this area has turned to the identification of genes related to important traits, such as fruit aroma volatiles. Of the ove...

    Authors: Gerardo Sánchez, Mónica Venegas-Calerón, Joaquín J Salas, Antonio Monforte, María L Badenes and Antonio Granell

    Citation: BMC Genomics 2013 14:343

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  7. Content type: Research article

    Interspecific hybridization creates individuals harboring diverged genomes. The interaction of these genomes can generate successful evolutionary novelty or disadvantageous genomic conflict. Annual sunflowers Hel...

    Authors: Heather C Rowe and Loren H Rieseberg

    Citation: BMC Genomics 2013 14:342

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  8. Content type: Research article

    The late blight pathogen Phytophthora infestans can attack both potato foliage and tubers. Although interaction transcriptome dynamics between potato foliage and various pathogens have been reported, no transcrip...

    Authors: Liangliang Gao, Zheng Jin Tu, Benjamin P Millett and James M Bradeen

    Citation: BMC Genomics 2013 14:340

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  9. Content type: Research article

    Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its di...

    Authors: Magda Aparecida Beneventi, Orzenil Bonfim da Silva Jr, Maria Eugênia Lisei de Sá, Alexandre Augusto Pereira Firmino, Regina Maria Santos de Amorim, Érika Valéria Saliba Albuquerque, Maria Cristina Mattar da Silva, Joseane Padilha da Silva, Magnólia de Araújo Campos, Marcus José Conceição Lopes, Roberto Coiti Togawa, Georgios Joanis Pappas Jr and Maria Fatima Grossi–de–Sa

    Citation: BMC Genomics 2013 14:322

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  10. Content type: Research article

    Leucine-rich repeat receptor-like kinases (LRR-RLKs) comprise the largest group within the receptor-like kinase (RLK) superfamily in plants. This gene family plays critical and diverse roles in plant growth, d...

    Authors: Yanjun Zan, Yan Ji, Yu Zhang, Shaohui Yang, Yingjin Song and Jiehua Wang

    Citation: BMC Genomics 2013 14:318

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  11. Content type: Research article

    Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives ...

    Authors: Kassa Semagn, Yoseph Beyene, Marilyn L Warburton, Amsal Tarekegne, Stephen Mugo, Barbara Meisel, Pierre Sehabiague and Boddupalli M Prasanna

    Citation: BMC Genomics 2013 14:313

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  12. Content type: Research article

    Auxin plays important roles in hormone crosstalk and the plant’s stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (...

    Authors: Huazhao Yuan, Kai Zhao, Hengjiu Lei, Xinjie Shen, Yun Liu, Xiong Liao and Tianhong Li

    Citation: BMC Genomics 2013 14:297

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  13. Content type: Research article

    Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countri...

    Authors: Jianxia Zhang, Kunlin Wu, Songjun Zeng, Jaime A Teixeira da Silva, Xiaolan Zhao, Chang-En Tian, Haoqiang Xia and Jun Duan

    Citation: BMC Genomics 2013 14:279

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  14. Content type: Research article

    Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular b...

    Authors: Harsh Raman, Rosy Raman, Andrzej Kilian, Frank Detering, Yan Long, David Edwards, Isobel AP Parkin, Andrew G Sharpe, Matthew N Nelson, Nick Larkan, Jun Zou, Jinling Meng, M Naveed Aslam, Jacqueline Batley, Wallace A Cowling and Derek Lydiate

    Citation: BMC Genomics 2013 14:277

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  15. Content type: Research article

    The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcripto...

    Authors: Shi-Hui Niu, Zhe-Xin Li, Hu-Wei Yuan, Xiao-Yang Chen, Yue Li and Wei Li

    Citation: BMC Genomics 2013 14:263

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  16. Content type: Research article

    The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacteri...

    Authors: Zahra-Katy Navabi, Terry Huebert, Andrew G Sharpe, Carmel M O’Neill, Ian Bancroft and Isobel AP Parkin

    Citation: BMC Genomics 2013 14:250

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  17. Content type: Research article

    Citrus huanglongbing (HLB) disease is caused by endogenous, phloem-restricted, Gram negative, uncultured bacteria named Candidatus Liberibacter africanus (CaLaf), Ca. L. asiaticus (CaLas), and Ca. L. americanus (...

    Authors: Valéria Mafra, Polyana K Martins, Carolina S Francisco, Marcelo Ribeiro-Alves, Juliana Freitas-Astúa and Marcos A Machado

    Citation: BMC Genomics 2013 14:247

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  18. Content type: Research article

    Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence...

    Authors: Chunfang Li, Yingjie Zhu, Xu Guo, Chao Sun, Hongmei Luo, Jingyuan Song, Ying Li, Lizhi Wang, Jun Qian and Shilin Chen

    Citation: BMC Genomics 2013 14:245

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  19. Content type: Research article

    Cotton (Gossypium hirsutum L.) is a major fiber crop that is grown worldwide; it faces extensive damage from sap-sucking insects, including aphids and whiteflies. Genome-wide transcriptome analysis was performed ...

    Authors: Neeraj Kumar Dubey, Ridhi Goel, Alok Ranjan, Asif Idris, Sunil Kumar Singh, Sumit K Bag, Krishnappa Chandrashekar, Kapil Deo Pandey, Pradhyumna Kumar Singh and Samir V Sawant

    Citation: BMC Genomics 2013 14:241

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  20. Content type: Research article

    Nicotianamine (NA), a ubiquitous molecule in plants, is an important metal ion chelator and the main precursor for phytosiderophores biosynthesis. Considerable progress has been achieved in cloning and charact...

    Authors: Xiaojin Zhou, Suzhen Li, Qianqian Zhao, Xiaoqing Liu, Shaojun Zhang, Cheng Sun, Yunliu Fan, Chunyi Zhang and Rumei Chen

    Citation: BMC Genomics 2013 14:238

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  21. Content type: Research article

    In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during wh...

    Authors: Saneyoshi Ueno, Christophe Klopp, Jean Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Léger, Elodie Prince, Antoine Kremer, Christophe Plomion and Grégoire Le Provost

    Citation: BMC Genomics 2013 14:236

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  22. Content type: Research article

    MicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) with a wide range of regulatory functions in plant development and stress responses. Although miRNAs associated with plant drought stress tolerance have bee...

    Authors: Peng Shuai, Dan Liang, Zhoujia Zhang, Weilun Yin and Xinli Xia

    Citation: BMC Genomics 2013 14:233

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  23. Content type: Research article

    Agarwood is an expensive resinous heartwood derived from Aquilaria plants that is widely used in traditional medicines, incense and perfume. Only wounded trees can produce agarwood, and the huge demand for the ag...

    Authors: Yanhong Xu, Zheng Zhang, Mengxi Wang, Jianhe Wei, Hongjiang Chen, Zhihui Gao, Chun Sui, Hongmei Luo, Xingli Zhang, Yun Yang, Hui Meng and Wenlan Li

    Citation: BMC Genomics 2013 14:227

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  24. Content type: Research article

    The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploid...

    Authors: Tatiana Belova, Bujie Zhan, Jonathan Wright, Mario Caccamo, Torben Asp, Hana Šimková, Matthew Kent, Christian Bendixen, Frank Panitz, Sigbjørn Lien, Jaroslav Doležel, Odd-Arne Olsen and Simen R Sandve

    Citation: BMC Genomics 2013 14:222

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  25. Content type: Research article

    Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from ...

    Authors: Ekrem Dündar, Öznur Suakar, Turgay Unver and Ayhan Dagdelen

    Citation: BMC Genomics 2013 14:219

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  26. Content type: Research article

    Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants suc...

    Authors: Peng Xu, Yimeng Kong, Xuan Li and Laigeng Li

    Citation: BMC Genomics 2013 14:217

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  27. Content type: Research article

    Transcription factors (TF) play a crucial role in regulating gene expression and are fit to regulate diverse cellular processes by interacting with other proteins. A TF named calmodulin binding transcription a...

    Authors: Neha Pandey, Alok Ranjan, Poonam Pant, Rajiv K Tripathi, Farha Ateek, Haushilla P Pandey, Uday V Patre and Samir V Sawant

    Citation: BMC Genomics 2013 14:216

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  28. Content type: Research article

    Phosphorus (P) is one of the essential but often limiting elements for plants. Based on transcriptional profiling we reported previously that more than 3,000 genes are differentially expressed between phosphat...

    Authors: Ping Lan, Wenfeng Li and Wolfgang Schmidt

    Citation: BMC Genomics 2013 14:210

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  29. Content type: Research article

    Transcription factor binding is regulated by several interactions, primarily involving cis-element binding. These binding sites maintain specificity by means of their sequence, and other additional factors such a...

    Authors: Rajesh Mehrotra, Sachin Sethi, Ipshita Zutshi, Purva Bhalothia and Sandhya Mehrotra

    Citation: BMC Genomics 2013 14:203

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  30. Content type: Research article

    Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influ...

    Authors: Md Shofiqul Islam, Bruno Studer, Stephen L Byrne, Jacqueline D Farrell, Frank Panitz, Christian Bendixen, Ian Max Møller and Torben Asp

    Citation: BMC Genomics 2013 14:202

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  31. Content type: Research article

    Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is a...

    Authors: Marcela Mendes Salazar, Leandro Costa Nascimento, Eduardo Leal Oliveira Camargo, Danieli Cristina Gonçalves, Jorge Lepikson Neto, Wesley Leoricy Marques, Paulo José Pereira Lima Teixeira, Piotr Mieczkowski, Jorge Maurício Costa Mondego, Marcelo Falsarella Carazzolle, Ana Carolina Deckmann and Gonçalo Amarante Guimarães Pereira

    Citation: BMC Genomics 2013 14:201

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  32. Content type: Research article

    Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg) Schwabe (teleomorph: Gibberellazeae Schwble), brings serious damage to wheat production. Chinese wheat landrace Wangshuibai is one of the mos...

    Authors: Jin Xiao, Xiahong Jin, Xinping Jia, Haiyan Wang, Aizhong Cao, Weiping Zhao, Haiyan Pei, Zhaokun Xue, Liqiang He, Qiguang Chen and Xiue Wang

    Citation: BMC Genomics 2013 14:197

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  33. Content type: Research article

    The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model le...

    Authors: Andrew G Sharpe, Larissa Ramsay, Lacey-Anne Sanderson, Michael J Fedoruk, Wayne E Clarke, Rong Li, Sateesh Kagale, Perumal Vijayan, Albert Vandenberg and Kirstin E Bett

    Citation: BMC Genomics 2013 14:192

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  34. Content type: Research article

    Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, ...

    Authors: Puneet Paul, Stefan Simm, Andreas Blaumeiser, Klaus-Dieter Scharf, Sotirios Fragkostefanakis, Oliver Mirus and Enrico Schleiff

    Citation: BMC Genomics 2013 14:189

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  35. Content type: Research article

    Cotton is the leading fiber crop worldwide. Gossypium barbadense is an important species of cotton because of its extra-long staple fibers with superior luster and silkiness. However, a systematic analysis and ut...

    Authors: Yuanda Lv, Liang Zhao, Xiaoyang Xu, Lei Wang, Cheng Wang, Tianzhen Zhang and Wangzhen Guo

    Citation: BMC Genomics 2013 14:170

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  36. Content type: Research article

    Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat...

    Authors: Dario Cantu, Baoju Yang, Randy Ruan, Kun Li, Virginia Menzo, Daolin Fu, Mawsheng Chern, Pamela C Ronald and Jorge Dubcovsky

    Citation: BMC Genomics 2013 14:166

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  37. Content type: Research article

    Pearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics ...

    Authors: Vengaldas Rajaram, Thirunavukkarasu Nepolean, Senapathy Senthilvel, Rajeev K Varshney, Vincent Vadez, Rakesh K Srivastava, Trushar M Shah, Ambawat Supriya, Sushil Kumar, Basava Ramana Kumari, Amindala Bhanuprakash, Mangamoori Lakshmi Narasu, Oscar Riera-Lizarazu and Charles Thomas Hash

    Citation: BMC Genomics 2013 14:159

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  38. Content type: Research article

    The length of cotton fiber is an important agronomic trait characteristic that directly affects the quality of yarn and fabric. The cotton (Gossypium hirsutum L.) fiber mutation, Ligon lintless-2, is controlled b...

    Authors: Marina Naoumkina, Doug J Hinchliffe, Rickie B Turley, John M Bland and David D Fang

    Citation: BMC Genomics 2013 14:155

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  39. Content type: Research article

    Biological nitrogen fixation in root nodules is a process of great importance to crops of soybean [Glycine max (L.) Merr.], as it may provide the bulk of the plant’s needs for nitrogen. Legume nodulation involves...

    Authors: Gesiele Almeida Barros de Carvalho, Jesiane Stefânia Silva Batista, Francismar Corrêa Marcelino-Guimarães, Leandro Costa do Nascimento and Mariangela Hungria

    Citation: BMC Genomics 2013 14:153

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  40. Content type: Research article

    Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centrom...

    Authors: Anupma Sharma, Thomas K Wolfgruber and Gernot G Presting

    Citation: BMC Genomics 2013 14:142

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  41. Content type: Research article

    MicroRNAs (miRNAs) are 20–21 nucleotide RNA molecules that suppress the transcription of target genes and may also inhibit translation. Despite the thousands of miRNAs identified and validated in numerous plan...

    Authors: Daiqing Huang, Chushin Koh, J Allan Feurtado, Edward WT Tsang and Adrian J Cutler

    Citation: BMC Genomics 2013 14:140

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  42. Content type: Research article

    Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior variet...

    Authors: Glenn T Howe, Jianbin Yu, Brian Knaus, Richard Cronn, Scott Kolpak, Peter Dolan, W Walter Lorenz and Jeffrey FD Dean

    Citation: BMC Genomics 2013 14:137

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  43. Content type: Research article

    Transcriptome analysis in combination with pathway-focused bioassays is suggested to be a helpful approach for gaining deeper insights into the complex mechanisms of action of herbal multicomponent preparation...

    Authors: Angela Klein, Oliver A Wrulich, Marcel Jenny, Peter Gruber, Kathrin Becker, Dietmar Fuchs, Johanna M Gostner and Florian Überall

    Citation: BMC Genomics 2013 14:133

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  44. Content type: Methodology article

    One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign sc...

    Authors: Dominik Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt

    Citation: BMC Genomics 2013 14:132

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