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 31 of 31

  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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

    Content type: Research article

    Published on:

  23. 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

    Content type: Research article

    Published on:

  24. 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

    Content type: Research article

    Published on:

  25. 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

    Content type: Research article

    Published on:

  26. 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

    Content type: Research article

    Published on:

  27. 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

    Content type: Research article

    Published on:

  28. 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

    Content type: Research article

    Published on:

  29. 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

    Content type: Research article

    Published on:

  30. 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

    Content type: Research article

    Published on:

  31. 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

    Content type: Research article

    Published on:

  32. 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

    Content type: Research article

    Published on:

  33. 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

    Content type: Research article

    Published on:

  34. 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

    Content type: Research article

    Published on:

  35. 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

    Content type: Research article

    Published on:

  36. 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

    Content type: Research article

    Published on:

  37. 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

    Content type: Research article

    Published on:

  38. 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

    Content type: Research article

    Published on:

  39. 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

    Content type: Research article

    Published on:

  40. 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

    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