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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 28 of 34

  1. Stem cells located in the centre of the shoot apical meristem are required for the repetitive formation of new organs such as leaves, branches and flowers. In Arabidopsis thaliana, the ZWILLE/PINHEAD/AGO10 (ZLL) ...

    Authors: Matthew R Tucker, Farshad Roodbarkelari, Elisabeth Truernit, Nikolai M Adamski, Annika Hinze, Barbara Lohmüller, Tobias Würschum and Thomas Laux

    Citation: BMC Genomics 2013 14:809

    Content type: Research article

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  2. Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited du...

    Authors: Shicheng Zhao, Pham Anh Tuan, Xiaohua Li, Yeon Bok Kim, HyeRan Kim, Chun Geon Park, Jingli Yang, Cheng Hao Li and Sang Un Park

    Citation: BMC Genomics 2013 14:802

    Content type: Research article

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  3. Plant microRNAs are short (~21 nt) non-coding molecules that regulate gene expression by targeting the mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cel...

    Authors: Anna Lukasik, Halina Pietrykowska, Leszek Paczek, Zofia Szweykowska-Kulinska and Piotr Zielenkiewicz

    Citation: BMC Genomics 2013 14:801

    Content type: Research article

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  4. One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow ...

    Authors: Mathilde Causse, Nelly Desplat, Laura Pascual, Marie-Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie Bérard, Rémi Bounon, Maria Tchoumakov, Dominique Brunel and Jean-Paul Bouchet

    Citation: BMC Genomics 2013 14:791

    Content type: Research article

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  5. Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of ...

    Authors: Jinyan Wang, Ping Lan, Huimin Gao, Lu Zheng, Wenfeng Li and Wolfgang Schmidt

    Citation: BMC Genomics 2013 14:783

    Content type: Research article

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  6. Changes in the copy number of DNA sequences are one of the main mechanisms generating genome variability in eukaryotes. These changes are often related to phenotypic effects such as genetic disorders or novel ...

    Authors: Víctor M González, Núria Aventín, Emilio Centeno and Pere Puigdomènech

    Citation: BMC Genomics 2013 14:782

    Content type: Research article

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  7. Many fruits, including watermelon, are proficient in carotenoid accumulation during ripening. While most genes encoding steps in the carotenoid biosynthetic pathway have been cloned, few transcriptional regula...

    Authors: Stefania Grassi, Gabriella Piro, Je Min Lee, Yi Zheng, Zhangjun Fei, Giuseppe Dalessandro, James J Giovannoni and Marcello S Lenucci

    Citation: BMC Genomics 2013 14:781

    Content type: Research article

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  8. The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and...

    Authors: Joseph I Said, Zhongxu Lin, Xianlong Zhang, Mingzhou Song and Jinfa Zhang

    Citation: BMC Genomics 2013 14:776

    Content type: Research article

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  9. Formation of compression (CW) and opposite wood (OW) in branches and bent trunks is an adaptive feature of conifer trees in response to various displacement forces, such as gravity, wind, snow and artificial b...

    Authors: Xinguo Li, Xiaohui Yang and Harry X Wu

    Citation: BMC Genomics 2013 14:768

    Content type: Research article

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  10. Plant calcium (Ca2+) signals are involved in a wide array of intracellular signalling pathways following pathogen invasion. Ca2+-binding sensory proteins such as Ca2+-dependent protein kinases (CPKs) have been pr...

    Authors: Chidananda Nagamangala Kanchiswamy, Tapan Kumar Mohanta, Andrea Capuzzo, Andrea Occhipinti, Francesca Verrillo, Massimo E Maffei and Mickael Malnoy

    Citation: BMC Genomics 2013 14:760

    Content type: Research article

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  11. AtPAP2 is a purple acid phosphatase that is targeted to both chloroplasts and mitochondria. Over-expression (OE) lines of AtPAP2 grew faster, produced more seeds, and contained higher leaf sucrose and glucose ...

    Authors: Feng Sun, Chao Liang, James Whelan, Jun Yang, Peng Zhang and Boon Leong Lim

    Citation: BMC Genomics 2013 14:752

    Content type: Research article

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  12. Peach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length...

    Authors: Jonathan Fresnedo-Ramírez, Pedro J Martínez-García, Dan E Parfitt, Carlos H Crisosto and Thomas M Gradziel

    Citation: BMC Genomics 2013 14:750

    Content type: Research article

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  13. The Himalayan or Indian Mayapple (Podophyllum hexandrum Royle) produces podophyllotoxin, which is used in the production of semisynthetic anticancer drugs. High throughput transcriptome sequences or genomic seque...

    Authors: Dipto Bhattacharyya, Ragini Sinha, Saptarshi Hazra, Riddhi Datta and Sharmila Chattopadhyay

    Citation: BMC Genomics 2013 14:748

    Content type: Research article

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  14. Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonans in the cell wall; their activity is regulated in part by pectin methylesterase inhibitors (PMEIs). PME activity may result...

    Authors: David Pinzón-Latorre and Michael K Deyholos

    Citation: BMC Genomics 2013 14:742

    Content type: Research article

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  15. The interaction between insect pests and their host plants is a never-ending race of evolutionary adaption. Plants have developed an armament against insect herbivore attacks, and attackers continuously learn ...

    Authors: Birgit Kersten, Andrea Ghirardo, Jörg-Peter Schnitzler, Basem Kanawati, Philippe Schmitt-Kopplin, Matthias Fladung and Hilke Schroeder

    Citation: BMC Genomics 2013 14:737

    Content type: Research article

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  16. Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Diant...

    Authors: Masafumi Yagi, Toshiya Yamamoto, Sachiko Isobe, Hideki Hirakawa, Satoshi Tabata, Koji Tanase, Hiroyasu Yamaguchi and Takashi Onozaki

    Citation: BMC Genomics 2013 14:734

    Content type: Research article

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  17. Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe is one of the most prevalent diseases of wheat (Triticum aestivum L.) and other small grain cereals. Resistance against the fungus is quantitative...

    Authors: Karl G Kugler, Gerald Siegwart, Thomas Nussbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus FX Mayer, Hermann Buerstmayr and Wolfgang Schweiger

    Citation: BMC Genomics 2013 14:728

    Content type: Research article

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  18. 'Kuerlexiangli’ (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit s...

    Authors: Xiaoxiao Qi, Jun Wu, Lifen Wang, Leiting Li, Yufen Cao, Luming Tian, Xingguang Dong and Shaoling Zhang

    Citation: BMC Genomics 2013 14:727

    Content type: Research article

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  19. Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thal...

    Authors: Pankaj Barah, Naresh Doni Jayavelu, Simon Rasmussen, Henrik Bjørn Nielsen, John Mundy and Atle M Bones

    Citation: BMC Genomics 2013 14:722

    Content type: Research article

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  20. Radish (Raphanus sativus L., 2n = 2× = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized...

    Authors: Di Shen, Honghe Sun, Mingyun Huang, Yi Zheng, Yang Qiu, Xixiang Li and Zhangjun Fei

    Citation: BMC Genomics 2013 14:721

    Content type: Research article

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  21. Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide associati...

    Authors: Shunmou Huang, Linbin Deng, Mei Guan, Jiana Li, Kun Lu, Hanzhong Wang, Donghui Fu, Annaliese S Mason, Shengyi Liu and Wei Hua

    Citation: BMC Genomics 2013 14:717

    Content type: Research article

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  22. MicroRNAs (miRNAs) are small, endogenously expressed, non-coding RNA molecules involved in gene transcription and expression that combine with specific mRNA site of target genes to inhibit protein synthesis or...

    Authors: Xuemei Chen, Wenhui Gao, Jinfa Zhang, Xianlong Zhang and Zhongxu Lin

    Citation: BMC Genomics 2013 14:706

    Content type: Research article

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  23. EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breedi...

    Authors: Ishminder K Mann, Jill L Wegrzyn and Om P Rajora

    Citation: BMC Genomics 2013 14:702

    Content type: Research article

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  24. Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are pa...

    Authors: Elena A Vidal, Tomás C Moyano, Gabriel Krouk, Manpreet S Katari, Milos Tanurdzic, W Richard McCombie, Gloria M Coruzzi and Rodrigo A Gutiérrez

    Citation: BMC Genomics 2013 14:701

    Content type: Research article

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  25. Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary mod...

    Authors: You-Jun Huang, Li-Li Liu, Jian-Qin Huang, Zheng-Jia Wang, Fang-Fang Chen, Qi-Xiang Zhang, Bing-Song Zheng and Ming Chen

    Citation: BMC Genomics 2013 14:691

    Content type: Research article

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  26. The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of whole genome ...

    Authors: Chaobo Tong, Xiaowu Wang, Jingyin Yu, Jian Wu, Wanshun Li, Junyan Huang, Caihua Dong, Wei Hua and Shengyi Liu

    Citation: BMC Genomics 2013 14:689

    Content type: Research article

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  27. Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacte...

    Authors: Li M Chen, Xin A Zhou, Wen B Li, Wei Chang, Rong Zhou, Cheng Wang, Ai H Sha, Zhi H Shan, Chan J Zhang, De Z Qiu, Zhong L Yang and Shui L Chen

    Citation: BMC Genomics 2013 14:687

    Content type: Research article

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  28. Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational appr...

    Authors: Lucia Natali, Rosa Maria Cossu, Elena Barghini, Tommaso Giordani, Matteo Buti, Flavia Mascagni, Michele Morgante, Navdeep Gill, Nolan C Kane, Loren Rieseberg and Andrea Cavallini

    Citation: BMC Genomics 2013 14:686

    Content type: Research article

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  29. Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been assoc...

    Authors: Mark W Davey, Ranganath Gudimella, Jennifer Ann Harikrishna, Lee Wan Sin, Norzulaani Khalid and Johan Keulemans

    Citation: BMC Genomics 2013 14:683

    Content type: Research article

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  30. The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of...

    Authors: Wenwei Xiong, Limei He, Yubin Li, Hugo K Dooner and Chunguang Du

    Citation: BMC Genomics 2013 14:679

    Content type: Software

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  31. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is one the most important citrus diseases, and affects all varieties of sweet orange (Citrus sinensis L. Osb). On the other hand, among the Citrus ...

    Authors: Carolina M Rodrigues, Alessandra A de Souza, Marco A Takita, Luciano T Kishi and Marcos A Machado

    Citation: BMC Genomics 2013 14:676

    Content type: Research article

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  32. Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased geno...

    Authors: Marco Ferrarini, Marco Moretto, Judson A Ward, Nada Šurbanovski, Vladimir Stevanović, Lara Giongo, Roberto Viola, Duccio Cavalieri, Riccardo Velasco, Alessandro Cestaro and Daniel J Sargent

    Citation: BMC Genomics 2013 14:670

    Content type: Research article

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  33. Crown gall (CG) (Agrobacterium tumefaciens) and the root lesion nematodes (RLNs) (Pratylenchus vulnus) are major challenges faced by the California walnut industry, reducing productivity and increasing the cost o...

    Authors: Sriema L Walawage, Monica T Britton, Charles A Leslie, Sandra L Uratsu, YingYue Li and Abhaya M Dandekar

    Citation: BMC Genomics 2013 14:668

    Content type: Research article

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  34. Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, B...

    Authors: Jingyin Yu, Meixia Zhao, Xiaowu Wang, Chaobo Tong, Shunmou Huang, Sadia Tehrim, Yumei Liu, Wei Hua and Shengyi Liu

    Citation: BMC Genomics 2013 14:664

    Content type: Database

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  35. Chrysanthemum is one of the most important ornamental crops in the world and drought stress seriously limits its production and distribution. In order to generate a functional genomics resource and obtain a de...

    Authors: Yanjie Xu, Shan Gao, Yingjie Yang, Mingyun Huang, Lina Cheng, Qian Wei, Zhangjun Fei, Junping Gao and Bo Hong

    Citation: BMC Genomics 2013 14:662

    Content type: Research article

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  36. The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology,...

    Authors: Richard S Fletcher, Jack L Mullen, Seth Yoder, William L Bauerle, Gretchen Reuning, Saunak Sen, Eli Meyer, Thomas E Juenger and John K McKay

    Citation: BMC Genomics 2013 14:655

    Content type: Methodology article

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  37. The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from w...

    Authors: Aziz Mithani, Eric J Belfield, Carly Brown, Caifu Jiang, Lindsey J Leach and Nicholas P Harberd

    Citation: BMC Genomics 2013 14:653

    Content type: Methodology article

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  38. Copy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organ...

    Authors: Ping Yu, Cai-Hong Wang, Qun Xu, Yue Feng, Xiao-Ping Yuan, Han-Yong Yu, Yi-Ping Wang, Sheng-Xiang Tang and Xing-Hua Wei

    Citation: BMC Genomics 2013 14:649

    Content type: Research article

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  39. Drought tolerance is an attribute maintained in plants by cross-talk between multiple and cascading metabolic pathways. Without a sequenced genome available for horse gram, it is difficult to comprehend such c...

    Authors: Jyoti Bhardwaj, Rohit Chauhan, Mohit Kumar Swarnkar, Rakesh Kumar Chahota, Anil Kumar Singh, Ravi Shankar and Sudesh Kumar Yadav

    Citation: BMC Genomics 2013 14:647

    Content type: Research article

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  40. Sunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii (Farlow) Berlese & de Toni is one of the major diseases of cultivated sunflowe...

    Authors: Maren Livaja, Yu Wang, Silke Wieckhorst, Grit Haseneyer, Michael Seidel, Volker Hahn, Steven J Knapp, Stefan Taudien, Chris-Carolin Schön and Eva Bauer

    Citation: BMC Genomics 2013 14:628

    Content type: Research article

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  41. Very little is known about manganese (Mn)-toxicity-responsive genes in citrus plants. Seedlings of ‘Xuegan’ (Citrus sinensis) and ‘Sour pummelo’ (Citrus grandis) were irrigated for 17 weeks with nutrient solution...

    Authors: Chen-Ping Zhou, Yi-Ping Qi, Xiang You, Lin-Tong Yang, Peng Guo, Xin Ye, Xin-Xing Zhou, Feng-Jiao Ke and Li-Song Chen

    Citation: BMC Genomics 2013 14:621

    Content type: Research article

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  42. Phakopsora pachyrhizi, the causal agent responsible for soybean rust, is among the top hundred most virulent plant pathogens and can cause soybean yield losses of up to 80% when appropriate conditions are met. We...

    Authors: Arianne Tremblay, Parsa Hosseini, Shuxian Li, Nadim W Alkharouf and Benjamin F Matthews

    Citation: BMC Genomics 2013 14:614

    Content type: Research article

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  43. Buffalograss [Buchloë dactyloides (Nutt.) Engel. syn. Bouteloua dactyloides (Nutt.) Columbus] is a United States native turfgrass species that requires less irrigation, fungicides and pesticides compared to more ...

    Authors: Michael Wachholtz, Tiffany Heng-Moss, Paul Twigg, Lisa Baird, Guoqing Lu and Keenan Amundsen

    Citation: BMC Genomics 2013 14:613

    Content type: Research article

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  44. Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nu...

    Authors: Hieu Xuan Cao and Renate Schmidt

    Citation: BMC Genomics 2013 14:603

    Content type: Methodology article

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  45. The yeast and human Pcf11 functions in both constitutive and regulated transcription and pre-mRNA processing. The constitutive roles of PCF11 are largely mediated by its direct interaction with RNA Polymerase ...

    Authors: Denghui Xing, Yajun Wang, Ruqiang Xu, Xinfu Ye, Dewei Yang and Qingshun Q Li

    Citation: BMC Genomics 2013 14:598

    Content type: Research article

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  46. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidops...

    Authors: Weiwei Deng, Diana M Buzas, Hua Ying, Masumi Robertson, Jennifer Taylor, William James Peacock, Elizabeth S Dennis and Chris Helliwell

    Citation: BMC Genomics 2013 14:593

    Content type: Research article

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