Skip to main content

Advertisement

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 31

  1. 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

    Content type: Research article

    Published on:

  2. 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

    Content type: Research article

    Published on:

  3. 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

    Content type: Research article

    Published on:

  4. 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

    Content type: Research article

    Published on:

  5. 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

    Content type: Research article

    Published on:

  6. 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

    Content type: Research article

    Published on:

  7. 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

    Content type: Research article

    Published on:

  8. 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

    Content type: Research article

    Published on:

  9. 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

    Content type: Research article

    Published on:

  10. 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

    Content type: Research article

    Published on:

  11. 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

    Content type: Research article

    Published on:

  12. 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

    Content type: Research article

    Published on:

  13. 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

    Content type: Database

    Published on:

  14. 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

    Content type: Research article

    Published on:

  15. 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

    Content type: Research article

    Published on:

  16. 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

    Content type: Research article

    Published on:

  17. 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

    Content type: Research article

    Published on:

  18. 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

    Content type: Research article

    Published on:

  19. 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

    Content type: Research article

    Published on:

  20. 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

    Content type: Research article

    Published on:

  21. 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

    Content type: Research article

    Published on:

  22. 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

    Content type: Database

    Published on:

  23. 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

    Content type: Methodology article

    Published on:

  24. 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

    Content type: Research article

    Published on:

  25. 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

    Content type: Research article

    Published on:

  26. 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

    Content type: Research article

    Published on:

  27. 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

    Content type: Research article

    Published on:

  28. 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

    Content type: Research article

    Published on:

  29. 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

    Content type: Research article

    Published on:

  30. 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

    Content type: Research article

    Published on:

  31. Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members...

    Authors: Frank M You, Naxin Huo, Karin R Deal, Yong Q Gu, Ming-Cheng Luo, Patrick E McGuire, Jan Dvorak and Olin D Anderson

    Citation: BMC Genomics 2011 12:59

    Content type: Methodology article

    Published on:

  32. The changes in storage reserve accumulation during maize (Zea mays L.) grain maturation are well established. However, the key molecular determinants controlling carbon flux to the grain and the partitioning of c...

    Authors: Hans Hartings, Massimiliano Lauria, Nadia Lazzaroni, Raul Pirona and Mario Motto

    Citation: BMC Genomics 2011 12:41

    Content type: Research article

    Published on:

  33. Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for ...

    Authors: Maria D Logacheva, Artem S Kasianov, Dmitriy V Vinogradov, Tagir H Samigullin, Mikhail S Gelfand, Vsevolod J Makeev and Aleksey A Penin

    Citation: BMC Genomics 2011 12:30

    Content type: Research article

    Published on:

  34. Ascochyta blight, caused by Mycosphaerella pinodes is one of the most important pea pathogens. However, little is known about the genes and mechanisms of resistance acting against M. pinodes in pea. Resistance id...

    Authors: Sara Fondevilla, Helge Küster, Franziska Krajinski, José I Cubero and Diego Rubiales

    Citation: BMC Genomics 2011 12:28

    Content type: Research article

    Published on:

  35. Cotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic map based on simple polymerase chain r...

    Authors: Yu Yu, Daojun Yuan, Shaoguang Liang, Ximei Li, Xiaqing Wang, Zhongxu Lin and Xianlong Zhang

    Citation: BMC Genomics 2011 12:15

    Content type: Research article

    Published on:

  36. Most agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by...

    Authors: Claude Urbany, Benjamin Stich, Lysann Schmidt, Ludwig Simon, Hergen Berding, Holger Junghans, Karl-Heinz Niehoff, Alexander Braun, Eckhard Tacke, Hans-Rheinhardt Hofferbert, Jens Lübeck, Josef Strahwald and Christiane Gebhardt

    Citation: BMC Genomics 2011 12:7

    Content type: Research article

    Published on:

  37. Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST colle...

    Authors: Isabelle Privat, Amélie Bardil, Aureliano Bombarely Gomez, Dany Severac, Christelle Dantec, Ivanna Fuentes, Lukas Mueller, Thierry Joët, David Pot, Séverine Foucrier, Stéphane Dussert, Thierry Leroy, Laurent Journot, Alexandre de Kochko, Claudine Campa, Marie-Christine Combes…

    Citation: BMC Genomics 2011 12:5

    Content type: Methodology article

    Published on:

  38. Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where gene...

    Authors: Yada Chutimanitsakun, Rick W Nipper, Alfonso Cuesta-Marcos, Luis Cistué, Ann Corey, Tanya Filichkina, Eric A Johnson and Patrick M Hayes

    Citation: BMC Genomics 2011 12:4

    Content type: Research article

    Published on:

  39. 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

    Content type: Research article

    Published on:

  40. 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

    Content type: Research article

    Published on:

  41. 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

    Content type: Research article

    Published on:

  42. 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

    Content type: Research article

    Published on:

  43. 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

    Content type: Methodology article

    Published on:

  44. 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

    Content type: Research article

    Published on:

  45. 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

    Content type: Research article

    Published on:

  46. 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

    Content type: Research article

    Published on:

2018 Journal Metrics

Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

Advertisement