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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 31 of 34

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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

    Content type: Methodology article

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  25. 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

    Content type: Database

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Methodology article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore th...

    Authors: Jinquan Li, Ann-Katrin Lühmann, Knuth Weißleder and Benjamin Stich

    Citation: BMC Genomics 2011 12:484

    Content type: Research article

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  38. The mechanical properties of wood are largely determined by the orientation of cellulose microfibrils in secondary cell walls. Several genes and their allelic variants have previously been found to affect micr...

    Authors: Xinguo Li, Harry X Wu and Simon G Southerton

    Citation: BMC Genomics 2011 12:480

    Content type: Research article

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  39. WRKY proteins are a large family of transcriptional regulators in higher plant. They are involved in many biological processes, such as plant development, metabolism, and responses to biotic and abiotic stress...

    Authors: Jian Ling, Weijie Jiang, Ying Zhang, Hongjun Yu, Zhenchuan Mao, Xingfang Gu, Sanwen Huang and Bingyan Xie

    Citation: BMC Genomics 2011 12:471

    Content type: Research article

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  40. Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the ear...

    Authors: Pei Xu, Xiaohua Wu, Jie Luo, Baogen Wang, Yonghua Liu, Jeffrey D Ehlers, Sha Wang, Zhongfu Lu and Guojing Li

    Citation: BMC Genomics 2011 12:467

    Content type: Research article

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  41. Photoperiod-sensitive genic male sterile (PGMS) rice, Nongken 58S, was discovered in 1973. It has been widely used for the production of hybrid rice, and great achievements have been made in improving rice yie...

    Authors: Wei Wang, Zhenwei Liu, Zhibin Guo, Gaoyuan Song, Qin Cheng, Daiming Jiang, Yingguo Zhu and Daichang Yang

    Citation: BMC Genomics 2011 12:462

    Content type: Research article

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  42. Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes ...

    Authors: Shaogui Guo, Jingan Liu, Yi Zheng, Mingyun Huang, Haiying Zhang, Guoyi Gong, Hongju He, Yi Ren, Silin Zhong, Zhangjun Fei and Yong Xu

    Citation: BMC Genomics 2011 12:454

    Content type: Research article

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  43. Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In add...

    Authors: Wenliang Wei, Xiaoqiong Qi, Linhai Wang, Yanxin Zhang, Wei Hua, Donghua Li, Haixia Lv and Xiurong Zhang

    Citation: BMC Genomics 2011 12:451

    Content type: Research article

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