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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 31

  1. 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

    Content type: Research article

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  2. 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

    Content type: Research article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Research article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Methodology article

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  9. Ramie fiber, extracted from vegetative organ stem bast, is one of the most important natural fibers. Understanding the molecular mechanisms of the vegetative growth of the ramie and the formation and developme...

    Authors: Touming Liu, Siyuan Zhu, Qingming Tang, Ping Chen, Yongting Yu and Shouwei Tang

    Citation: BMC Genomics 2013 14:125

    Content type: Research article

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  10. High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution...

    Authors: Régine Delourme, Cyril Falentin, Berline Fopa Fomeju, Marie Boillot, Gilles Lassalle, Isabelle André, Jorge Duarte, Valérie Gauthier, Nicole Lucante, Amandine Marty, Maryline Pauchon, Jean-Philippe Pichon, Nicolas Ribière, Gwenn Trotoux, Philippe Blanchard, Nathalie Rivière…

    Citation: BMC Genomics 2013 14:120

    Content type: Research article

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  11. Plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, an...

    Authors: Hongjian Wan, Wei Yuan, Kailiang Bo, Jia Shen, Xin Pang and Jinfeng Chen

    Citation: BMC Genomics 2013 14:109

    Content type: Research article

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  12. Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the...

    Authors: Chaotian Xie, Bing Li, Yan Xu, Dehua Ji and Changsheng Chen

    Citation: BMC Genomics 2013 14:107

    Content type: Research article

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  13. White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes. The apparent existence of highly similar homeolog copies for the majority of genes in white c...

    Authors: Istvan Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T Abberton and Dan Milbourne

    Citation: BMC Genomics 2013 14:100

    Content type: Research article

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  14. Cotton (Gossypium hirsutum) anther development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. However, only a small number of genes are known to be specifically involv...

    Authors: Mingming Wei, Meizhen Song, Shuli Fan and Shuxun Yu

    Citation: BMC Genomics 2013 14:97

    Content type: Research article

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  15. Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infectio...

    Authors: Reena Narsai, Chuang Wang, Jie Chen, Jianli Wu, Huixia Shou and James Whelan

    Citation: BMC Genomics 2013 14:93

    Content type: Research article

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  16. The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. ang...

    Authors: Michał Książkiewicz, Katarzyna Wyrwa, Anna Szczepaniak, Sandra Rychel, Karolina Majcherkiewicz, Łucja Przysiecka, Wojciech Karlowski, Bogdan Wolko and Barbara Naganowska

    Citation: BMC Genomics 2013 14:79

    Content type: Research article

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  17. Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in ...

    Authors: Marco A N Passos, Viviane Oliveira de Cruz, Flavia L Emediato, Cristiane Camargo de Teixeira, Vânia C Rennó Azevedo, Ana C M Brasileiro, Edson P Amorim, Claudia F Ferreira, Natalia F Martins, Roberto C Togawa, Georgios J Pappas Júnior, Orzenil Bonfim da Silva Jr and Robert NG Miller

    Citation: BMC Genomics 2013 14:78

    Content type: Research article

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  18. Phosphorus (P) is an essential macronutrient for plant growth and development. To modulate their P homeostasis, plants must balance P uptake, mobilisation, and partitioning to various organs. Despite the world...

    Authors: Youko Oono, Fuminori Kobayashi, Yoshihiro Kawahara, Takayuki Yazawa, Hirokazu Handa, Takeshi Itoh and Takashi Matsumoto

    Citation: BMC Genomics 2013 14:77

    Content type: Research article

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  19. Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical ...

    Authors: Ahmad Yamin Abdul Rahman, Abhilash O Usharraj, Biswapriya B Misra, Gincy P Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz…

    Citation: BMC Genomics 2013 14:75

    Content type: Research article

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  20. Class 2 transposable elements (TEs) are the predominant elements in and around plant genes where they generate significant allelic diversity. Using the complete sequences of four grasses, we have performed a n...

    Authors: Yujun Han, Shanshan Qin and Susan R Wessler

    Citation: BMC Genomics 2013 14:71

    Content type: Research article

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  21. Phosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean lea...

    Authors: Feng Xu, Qian Liu, Luying Chen, Jiebin Kuang, Thomas Walk, Jinxiang Wang and Hong Liao

    Citation: BMC Genomics 2013 14:66

    Content type: Research article

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  22. Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered i...

    Authors: Megumi Kasai, Hideo Matsumura, Kentaro Yoshida, Ryohei Terauchi, Akito Taneda and Akira Kanazawa

    Citation: BMC Genomics 2013 14:63

    Content type: Research article

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  23. Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture...

    Authors: Giorgio Pea, Htay Htay Aung, Elisabetta Frascaroli, Pierangelo Landi and Mario Enrico Pè

    Citation: BMC Genomics 2013 14:61

    Content type: Research article

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  24. Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lyc...

    Authors: Riccardo Aiese Cigliano, Walter Sanseverino, Gaetana Cremona, Maria R Ercolano, Clara Conicella and Federica M Consiglio

    Citation: BMC Genomics 2013 14:57

    Content type: Research article

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  25. Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at pr...

    Authors: Zhen Qin, Zhengqiu Cai, Guangmin Xia and Mengcheng Wang

    Citation: BMC Genomics 2013 14:56

    Content type: Research article

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  26. Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to dis...

    Authors: Luca Venturini, Alberto Ferrarini, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Silvia Dal Santo, Andrea Minio, Genny Buson, Paola Tononi, Elisa Debora Zago, Gianpiero Zamperin, Diana Bellin, Mario Pezzotti and Massimo Delledonne

    Citation: BMC Genomics 2013 14:41

    Content type: Research article

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  27. The outer cell wall of the pollen grain (exine) is an extremely resistant structure containing sporopollenin, a mixed polymer made up of fatty acids and phenolic compounds. The synthesis of sporopollenin in th...

    Authors: Gabino Ríos, Francisco R Tadeo, Carmen Leida and María L Badenes

    Citation: BMC Genomics 2013 14:40

    Content type: Research article

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  28. MicroRNAs (miRNAs) regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal of great economic importance, very little data is available concerning its miRNA bioge...

    Authors: Katarzyna Kruszka, Andrzej Pacak, Aleksandra Swida-Barteczka, Agnieszka K Stefaniak, Elzbieta Kaja, Izabela Sierocka, Wojciech Karlowski, Artur Jarmolowski and Zofia Szweykowska-Kulinska

    Citation: BMC Genomics 2013 14:34

    Content type: Research article

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  29. Rubber tree (Hevea brasiliensis) laticifers are the source of natural rubber. Rubber production depends on endogenous and exogenous ethylene (ethephon). AP2/ERF transcription factors, and especially Ethylene-Resp...

    Authors: Cuifang Duan, Xavier Argout, Virginie Gébelin, Marilyne Summo, Jean-François Dufayard, Julie Leclercq, Kuswanhadi, Piyanuch Piyatrakul, Julien Pirrello, Maryannick Rio, Antony Champion and Pascal Montoro

    Citation: BMC Genomics 2013 14:30

    Content type: Research article

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  30. Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress impos...

    Authors: Zhen-hua Dang, Lin-lin Zheng, Jia Wang, Zhe Gao, Shu-biao Wu, Zhi Qi and Ying-chun Wang

    Citation: BMC Genomics 2013 14:29

    Content type: Research article

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  31. Red colour in kiwifruit results from the presence of anthocyanin pigments. Their expression, however, is complex, and varies among genotypes, species, tissues and environments. An understanding of the biosynth...

    Authors: Lena G Fraser, Alan G Seal, Mirco Montefiori, Tony K McGhie, Gianna K Tsang, Paul M Datson, Elena Hilario, Hinga E Marsh, Juanita K Dunn, Roger P Hellens, Kevin M Davies, Mark A McNeilage, H Nihal De Silva and Andrew C Allan

    Citation: BMC Genomics 2013 14:28

    Content type: Research article

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  32. Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousa...

    Authors: Zhi-Liang Zheng and Yihong Zhao

    Citation: BMC Genomics 2013 14:27

    Content type: Research article

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  33. The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulat...

    Authors: Xiaohong Yan, Caihua Dong, Jingyin Yu, Wanghui Liu, Chenghong Jiang, Jia Liu, Qiong Hu, Xiaoping Fang and Wenhui Wei

    Citation: BMC Genomics 2013 14:26

    Content type: Research article

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  34. Salinity inhibits growth and development of most plants. The response to salinity is complex and varies between plant organs and stages of development. It involves challenges of ion toxicities and deficiencies...

    Authors: Michael Kravchik and Nirit Bernstein

    Citation: BMC Genomics 2013 14:24

    Content type: Research article

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  35. Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focuse...

    Authors: Rongrong Zhai, Yue Feng, Huimin Wang, Xiaodeng Zhan, Xihong Shen, Weiming Wu, Yingxin Zhang, Daibo Chen, Gaoxing Dai, Zhanlie Yang, Liyong Cao and Shihua Cheng

    Citation: BMC Genomics 2013 14:19

    Content type: Research article

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  36. Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breedin...

    Authors: Pedro IT Silva, Alexandre M Martins, Ediene G Gouvea, Marco Pessoa-Filho and Márcio E Ferreira

    Citation: BMC Genomics 2013 14:17

    Content type: Research article

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  37. A reciprocal recurrent selection program has been under way for the Coffea canephora coffee tree for approximately thirty years in the Ivory Coast. Association genetics would help to speed up this program by more...

    Authors: Philippe Cubry, Fabien de Bellis, Komlan Avia, Sophie Bouchet, David Pot, Magali Dufour, Hyacinthe Legnate and Thierry Leroy

    Citation: BMC Genomics 2013 14:10

    Content type: Research article

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  38. Regulatory network of cytoplasmic male sterility (CMS) occurrence is still largely unknown in plants, although numerous researches have been attempted to isolate genes involved in CMS. Here, we employed high-t...

    Authors: Jinghua Yang, Xunyan Liu, Baochen Xu, Na Zhao, Xiaodong Yang and Mingfang Zhang

    Citation: BMC Genomics 2013 14:9

    Content type: Research article

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  39. Water and nitrogen are two of the most critical inputs required to achieve the high yield potential of modern corn varieties. Under most agricultural settings however they are often scarce and costly. Fortunat...

    Authors: Sabrina Humbert, Sanjeena Subedi, Jonathan Cohn, Bin Zeng, Yong-Mei Bi, Xi Chen, Tong Zhu, Paul D McNicholas and Steven J Rothstein

    Citation: BMC Genomics 2013 14:3

    Content type: Research article

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  40. Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping...

    Authors: Judson A Ward, Jasbir Bhangoo, Felicidad Fernández-Fernández, Patrick Moore, JD Swanson, Roberto Viola, Riccardo Velasco, Nahla Bassil, Courtney A Weber and Daniel J Sargent

    Citation: BMC Genomics 2013 14:2

    Content type: Research article

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  41. Cluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no tran...

    Authors: Chiara Pastore, Sara Zenoni, Giovanni Battista Tornielli, Gianluca Allegro, Silvia Dal Santo, Gabriele Valentini, Cesare Intrieri, Mario Pezzotti and Ilaria Filippetti

    Citation: BMC Genomics 2011 12:631

    Content type: Research article

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  42. As a newly identified category of DNA transposon, helitrons have been found in a large number of eukaryotes genomes. Helitrons have contributed significantly to the intra-specific genome diversity in maize. Altho...

    Authors: Yongbin Dong, Xiaomin Lu, Weibin Song, Lei Shi, Mei Zhang, Hainan Zhao, Yinping Jiao and Jinsheng Lai

    Citation: BMC Genomics 2011 12:609

    Content type: Research article

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  43. In trees, a substantial amount of carbon is directed towards production of phenolics for development and defense. This metabolic pathway is also a major factor in resistance to insect pathogens in spruce. In s...

    Authors: Ilga Porth, Björn Hamberger, Richard White and Kermit Ritland

    Citation: BMC Genomics 2011 12:608

    Content type: Research article

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  44. Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development ...

    Authors: Jan M de Boer, Theo JA Borm, Taco Jesse, Bart Brugmans, Xiaomin Tang, Glenn J Bryan, Jaap Bakker, Herman J van Eck and Richard GF Visser

    Citation: BMC Genomics 2011 12:594

    Content type: Research article

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  45. The nonautonomous maize Ds transposons can only move in the presence of the autonomous element Ac. They comprise a heterogeneous group that share 11-bp terminal inverted repeats (TIRs) and some subterminal repeat...

    Authors: Chunguang Du, Andrew Hoffman, Limei He, Jason Caronna and Hugo K Dooner

    Citation: BMC Genomics 2011 12:588

    Content type: Research article

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