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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 27 of 30

  1. Content type: Research article

    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

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  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Research article

    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

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  5. Content type: Research article

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Research article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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  12. Content type: Research article

    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

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  13. Content type: Research article

    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

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

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  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Methodology article

    Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptom...

    Authors: Jörg Toepel, Stefan P Albaum, Samuel Arvidsson, Alexander Goesmann, Marco la Russa, Kristin Rogge and Olaf Kruse

    Citation: BMC Genomics 2011 12:579

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  33. Content type: Database

    The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced usi...

    Authors: Riaz Ahmad, Dan E Parfitt, Joseph Fass, Ebenezer Ogundiwin, Amit Dhingra, Thomas M Gradziel, Dawei Lin, Nikhil A Joshi, Pedro J Martinez-Garcia and Carlos H Crisosto

    Citation: BMC Genomics 2011 12:569

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  34. Content type: Research article

    Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias,...

    Authors: Wenxuan Liu, Supaphan Thummasuwan, Sunish K Sehgal, Philippe Chouvarine and Daniel G Peterson

    Citation: BMC Genomics 2011 12:553

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  35. Content type: Research article

    Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The ...

    Authors: Chun Sui, Jie Zhang, Jianhe Wei, Shilin Chen, Ying Li, Jiesen Xu, Yue Jin, Caixiang Xie, Zhihui Gao, Hongjiang Chen, Chengmin Yang, Zheng Zhang and Yanhong Xu

    Citation: BMC Genomics 2011 12:539

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  36. Content type: Research article

    In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantat...

    Authors: Emilie Villar, Christophe Klopp, Céline Noirot, Evandro Novaes, Matias Kirst, Christophe Plomion and Jean-Marc Gion

    Citation: BMC Genomics 2011 12:538

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  37. Content type: Research article

    Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which exhibits clinical e...

    Authors: Yongzhen Sun, Hongmei Luo, Ying Li, Chao Sun, Jingyuan Song, Yunyun Niu, Yingjie Zhu, Liang Dong, Aiping Lv, Enzo Tramontano and Shilin Chen

    Citation: BMC Genomics 2011 12:533

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  38. Content type: Research article

    Soybean is a valuable crop that provides protein and oil. Soybean requires a large amount of nitrogen (N) to accumulate high levels of N in the seed. The yield and protein content of soybean seeds are directly...

    Authors: Qing N Hao, Xin A Zhou, Ai H Sha, Cheng Wang, Rong Zhou and Shui L Chen

    Citation: BMC Genomics 2011 12:525

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  39. Content type: Research article

    Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. R...

    Authors: Ling-Ling Gao, James K Hane, Lars G Kamphuis, Rhonda Foley, Bu-Jun Shi, Craig A Atkins and Karam B Singh

    Citation: BMC Genomics 2011 12:521

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  40. Content type: Research article

    Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditio...

    Authors: Diana V Dugas, Marcela K Monaco, Andrew Olson, Robert R Klein, Sunita Kumari, Doreen Ware and Patricia E Klein

    Citation: BMC Genomics 2011 12:514

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  41. Content type: Methodology article

    Wheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed matura...

    Authors: Xinglu Yang, Hongliang Xu, Wenhui Li, Le Li, Jinyue Sun, Yaxuan Li, Yueming Yan and Yingkao Hu

    Citation: BMC Genomics 2011 12:513

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  42. Content type: Research article

    Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, dow...

    Authors: Falah As-sadi, Sébastien Carrere, Quentin Gascuel, Thibaut Hourlier, David Rengel, Marie-Christine Le Paslier, Amandine Bordat, Marie-Claude Boniface, Dominique Brunel, Jérôme Gouzy, Laurence Godiard and Patrick Vincourt

    Citation: BMC Genomics 2011 12:498

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  43. Content type: Research article

    Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these ca...

    Authors: Shengxin Chang, Tiantian Yang, Tongqing Du, Yongjuan Huang, Jianmei Chen, Jiyong Yan, Jianbo He and Rongzhan Guan

    Citation: BMC Genomics 2011 12:497

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  44. Content type: Research article

    Increasing the nutrient concentration of wheat grains is important to ameliorate nutritional deficiencies in many parts of the world. Proteins and nutrients in the wheat grain are largely derived from the remo...

    Authors: Dario Cantu, Stephen P Pearce, Assaf Distelfeld, Michael W Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima and Jorge Dubcovsky

    Citation: BMC Genomics 2011 12:492

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