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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 34

  1. Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient for...

    Authors: Stephen M Gross, Jeffrey A Martin, June Simpson, María Jazmín Abraham-Juarez, Zhong Wang and Axel Visel

    Citation: BMC Genomics 2013 14:563

    Content type: Research article

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  2. Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quali...

    Authors: Zhongxiong Lai and Yuling Lin

    Citation: BMC Genomics 2013 14:561

    Content type: Research article

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  3. Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflowe...

    Authors: Venkatramana Pegadaraju, Rick Nipper, Brent Hulke, Lili Qi and Quentin Schultz

    Citation: BMC Genomics 2013 14:556

    Content type: Research article

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  4. Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cel...

    Authors: Rongrong Guo, Xiaozhao Xu, Bassett Carole, Xiaoqin Li, Min Gao, Yi Zheng and Xiping Wang

    Citation: BMC Genomics 2013 14:554

    Content type: Research article

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  5. Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the mo...

    Authors: Caiqin Li, Yan Wang, Xuming Huang, Jiang Li, Huicong Wang and Jianguo Li

    Citation: BMC Genomics 2013 14:552

    Content type: Research article

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  6. Larix gmelinii is a dominant tree species in China’s boreal forests and plays an important role in the coniferous ecosystem. It is also one of the most economically important tree species in the Chinese timber in...

    Authors: Lina Men, Shanchun Yan and Guanjun Liu

    Citation: BMC Genomics 2013 14:548

    Content type: Research article

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  7. Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nemato...

    Authors: Paolo Bagnaresi, Tea Sala, Tiziana Irdani, Cristina Scotto, Antonella Lamontanara, Massimiliano Beretta, Giuseppe Leonardo Rotino, Sara Sestili, Luigi Cattivelli and Emidio Sabatini

    Citation: BMC Genomics 2013 14:540

    Content type: Research article

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  8. Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in m...

    Authors: Jin Zhang, Jianbo Li, Bobin Liu, Li Zhang, Jun Chen and Mengzhu Lu

    Citation: BMC Genomics 2013 14:532

    Content type: Research article

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  9. After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried...

    Authors: Han Xia, Chuanzhi Zhao, Lei Hou, Aiqin Li, Shuzhen Zhao, Yuping Bi, Jing An, Yanxiu Zhao, Shubo Wan and Xingjun Wang

    Citation: BMC Genomics 2013 14:517

    Content type: Research article

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  10. Aphids are among the most destructive pests in temperate climates, causing significant damage on several crops including tomato. We carried out a transcriptomic and proteomic study to get insights into the mol...

    Authors: Valentina Coppola, Mariangela Coppola, Mariapina Rocco, Maria Cristina Digilio, Chiara D’Ambrosio, Giovanni Renzone, Rosanna Martinelli, Andrea Scaloni, Francesco Pennacchio, Rosa Rao and Giandomenico Corrado

    Citation: BMC Genomics 2013 14:515

    Content type: Research article

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  11. Argonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese...

    Authors: Fenjuan Shao and Shanfa Lu

    Citation: BMC Genomics 2013 14:512

    Content type: Research article

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  12. The root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to ...

    Authors: Xiaoxia Ma, Chaogang Shao, Huizhong Wang, Yongfeng Jin and Yijun Meng

    Citation: BMC Genomics 2013 14:510

    Content type: Research article

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  13. The moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usabilit...

    Authors: Andreas D Zimmer, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A Rensing and Ralf Reski

    Citation: BMC Genomics 2013 14:498

    Content type: Research article

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  14. Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long bee...

    Authors: Xingfei Zheng, Cheng Pan, Ying Diao, Yongning You, Chaozhu Yang and Zhongli Hu

    Citation: BMC Genomics 2013 14:490

    Content type: Research article

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  15. Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as −30°C during the winter. Although A. mongolicus is an id...

    Authors: Tao Pang, Chu-Yu Ye, Xinli Xia and Weilun Yin

    Citation: BMC Genomics 2013 14:488

    Content type: Research article

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  16. Two plant-specific transcription factors, NAC and YABBY, are involved in important plant developmental processes. However their molecular mechanisms, especially DNA binding sites and co-regulated genes, are la...

    Authors: Md Shamimuzzaman and Lila Vodkin

    Citation: BMC Genomics 2013 14:477

    Content type: Research article

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  17. Genlisea aurea (Lentibulariaceae) is a carnivorous plant with unusually small genome size - 63.6 Mb – one of the smallest known among higher plants. Data on the genome sizes and the phylogeny of Genlisea suggest ...

    Authors: Evgeny V Leushkin, Roman A Sutormin, Elena R Nabieva, Aleksey A Penin, Alexey S Kondrashov and Maria D Logacheva

    Citation: BMC Genomics 2013 14:476

    Content type: Research article

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  18. Next generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with ...

    Authors: Juan J Gutierrez-Gonzalez, Zheng Jin Tu and David F Garvin

    Citation: BMC Genomics 2013 14:471

    Content type: Research article

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  19. Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Usi...

    Authors: Kumar Paritosh, Satish K Yadava, Vibha Gupta, Priya Panjabi-Massand, Yashpal S Sodhi, Akshay K Pradhan and Deepak Pental

    Citation: BMC Genomics 2013 14:463

    Content type: Research article

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  20. The number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root format...

    Authors: Nurit Firon, Don LaBonte, Arthur Villordon, Yanir Kfir, Julio Solis, Evgenia Lapis, Temima Schnitzer Perlman, Adi Doron-Faigenboim, Amots Hetzroni, Leviah Althan and Lahan Adani Nadir

    Citation: BMC Genomics 2013 14:460

    Content type: Research article

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  21. Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genoty...

    Authors: Daryl T Morishige, Patricia E Klein, Josie L Hilley, Sayed Mohammad Ebrahim Sahraeian, Arun Sharma and John E Mullet

    Citation: BMC Genomics 2013 14:448

    Content type: Methodology article

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  22. Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is curren...

    Authors: Urte Schlüter, Christian Colmsee, Uwe Scholz, Andrea Bräutigam, Andreas PM Weber, Nina Zellerhoff, Marcel Bucher, Holger Fahnenstich and Uwe Sonnewald

    Citation: BMC Genomics 2013 14:442

    Content type: Research article

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  23. Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so a...

    Authors: Julie King, Ann Thomas, Caron James, Ian King and Ian Armstead

    Citation: BMC Genomics 2013 14:437

    Content type: Research article

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  24. Calcium-dependent protein kinases (CDPKs) have been shown to play important roles in various physiological processes, including plant growth and development, abiotic and biotic stress responses and plant hormo...

    Authors: Xiangpei Kong, Wei Lv, Shanshan Jiang, Dan Zhang, Guohua Cai, Jiaowen Pan and Dequan Li

    Citation: BMC Genomics 2013 14:433

    Content type: Research article

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  25. Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effec...

    Authors: Andrea Visioni, Alessandro Tondelli, Enrico Francia, Alexander Pswarayi, Marcos Malosetti, Joanne Russell, William Thomas, Robbie Waugh, Nicola Pecchioni, Ignacio Romagosa and Jordi Comadran

    Citation: BMC Genomics 2013 14:424

    Content type: Research article

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  26. Wheat – Hessian fly interaction follows a typical gene-for-gene model. Hessian fly larvae die in wheat plants carrying an effective resistance gene, or thrive in susceptible plants that carry no effective resi...

    Authors: Chitvan Khajuria, Haiyan Wang, Xuming Liu, Shanda Wheeler, John C Reese, Mustapha El Bouhssini, R Jeff Whitworth and Ming-Shun Chen

    Citation: BMC Genomics 2013 14:423

    Content type: Research article

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  27. Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Change...

    Authors: Xin-Chao Wang, Qiong-Yi Zhao, Chun-Lei Ma, Zong-Hong Zhang, Hong-Li Cao, Yi-Meng Kong, Chuan Yue, Xin-Yuan Hao, Liang Chen, Jian-Qiang Ma, Ji-Qiang Jin, Xuan Li and Ya-Jun Yang

    Citation: BMC Genomics 2013 14:415

    Content type: Research article

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  28. Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or ot...

    Authors: Matthew K Gilbert, Rickie B Turley, Hee Jin Kim, Ping Li, Gregory Thyssen, Yuhong Tang, Christopher D Delhom, Marina Naoumkina and David D Fang

    Citation: BMC Genomics 2013 14:403

    Content type: Research article

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  29. Understanding the genetic architecture of quantitative traits is important for developing genome-based crop improvement methods. Genome-wide association study (GWAS) is a powerful technique for mining novel fu...

    Authors: Satish Kumar, Dorian J Garrick, Marco CAM Bink, Claire Whitworth, David Chagné and Richard K Volz

    Citation: BMC Genomics 2013 14:393

    Content type: Research article

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  30. Eukaryotic mitogen-activated protein kinase (MAPK/MPK) signaling cascades transduce and amplify environmental signals via three types of reversibly phosphorylated kinases to activate defense gene expression. C...

    Authors: Wanwan Liang, Bo Yang, Bao-Jun Yu, Zili Zhou, Cui Li, Ming Jia, Yun Sun, Yue Zhang, Feifei Wu, Hanfeng Zhang, Boya Wang, Michael K Deyholos and Yuan-Qing Jiang

    Citation: BMC Genomics 2013 14:392

    Content type: Research article

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  31. White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available,...

    Authors: Andrew G Griffiths, Brent A Barrett, Deborah Simon, Anar K Khan, Paul Bickerstaff, Craig B Anderson, Benjamin K Franzmayr, Kerry R Hancock and Chris S Jones

    Citation: BMC Genomics 2013 14:388

    Content type: Research article

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  32. The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees...

    Authors: Julien Prunier, Betty Pelgas, France Gagnon, Mireille Desponts, Nathalie Isabel, Jean Beaulieu and Jean Bousquet

    Citation: BMC Genomics 2013 14:368

    Content type: Research article

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  33. Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have...

    Authors: Erin L McAdam, Jules S Freeman, Simon P Whittock, Emily J Buck, Jernej Jakse, Andreja Cerenak, Branka Javornik, Andrzej Kilian, Cai-Hong Wang, Dave Andersen, René E Vaillancourt, Jason Carling, Ron Beatson, Lawrence Graham, Donna Graham, Peter Darby…

    Citation: BMC Genomics 2013 14:360

    Content type: Research article

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  34. Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-w...

    Authors: Hua Bao, Eryang Li, Shawn D Mansfield, Quentin CB Cronk, Yousry A El-Kassaby and Carl J Douglas

    Citation: BMC Genomics 2013 14:359

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

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