Skip to main content

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 25 of 34

  1. Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synth...

    Authors: Kai Guo, Weihua Zou, Yongqing Feng, Mingliang Zhang, Jing Zhang, Fen Tu, Guosheng Xie, Lingqiang Wang, Yangting Wang, Sebastian Klie, Staffan Persson and Liangcai Peng

    Citation: BMC Genomics 2014 15:596

    Content type: Research article

    Published on:

  2. Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To...

    Authors: Shubhra Rastogi, Seema Meena, Ankita Bhattacharya, Sumit Ghosh, Rakesh Kumar Shukla, Neelam Singh Sangwan, Raj Kishori Lal, Madan Mohan Gupta, Umesh Chandra Lavania, Vikrant Gupta, Dinesh A Nagegowda and Ajit Kumar Shasany

    Citation: BMC Genomics 2014 15:588

    Content type: Research article

    Published on:

  3. Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as suffere...

    Authors: Gina Cannarozzi, Sonia Plaza-Wüthrich, Korinna Esfeld, Stéphanie Larti, Yi Song Wilson, Dejene Girma, Edouard de Castro, Solomon Chanyalew, Regula Blösch, Laurent Farinelli, Eric Lyons, Michel Schneider, Laurent Falquet, Cris Kuhlemeier, Kebebew Assefa and Zerihun Tadele

    Citation: BMC Genomics 2014 15:581

    Content type: Research article

    Published on:

  4. Agarwood is derived from Aquilaria trees, the trade of which has come under strict control with a listing in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. ...

    Authors: Chuan-Hung Chen, Tony Chien-Yen Kuo, Meng-Han Yang, Ting-Ying Chien, Mei-Ju Chu, Li-Chun Huang, Chien-Yu Chen, Hsiao-Feng Lo, Shih-Tong Jeng and Long-Fang O Chen

    Citation: BMC Genomics 2014 15:578

    Content type: Research article

    Published on:

  5. Stevia (Stevia rebaudiana) is an important medicinal plant that yields diterpenoid steviol glycosides (SGs). SGs are currently used in the preparation of medicines, food products and neutraceuticals because of it...

    Authors: Junwen Chen, Kai Hou, Peng Qin, Hongchang Liu, Bin Yi, Wenting Yang and Wei Wu

    Citation: BMC Genomics 2014 15:571

    Content type: Research article

    Published on:

  6. Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS...

    Authors: Yeong Deuk Jo, Yoomi Choi, Dong-Hwan Kim, Byung-Dong Kim and Byoung-Cheorl Kang

    Citation: BMC Genomics 2014 15:561

    Content type: Research article

    Published on:

  7. Homoeologous sequences pose a particular challenge if bacterial artificial chromosome (BAC) contigs shall be established for specific regions of an allopolyploid genome. Single nucleotide polymorphisms (SNPs) ...

    Authors: Hieu Xuan Cao and Renate Schmidt

    Citation: BMC Genomics 2014 15:560

    Content type: Methodology article

    Published on:

  8. Marker-assisted selection (MAS) and genomic selection (GS) based on genome-wide marker data provide powerful tools to predict the genotypic value of selection material in plant breeding. However, case-to-case ...

    Authors: Yu Wang, Michael Florian Mette, Thomas Miedaner, Marlen Gottwald, Peer Wilde, Jochen C Reif and Yusheng Zhao

    Citation: BMC Genomics 2014 15:556

    Content type: Research article

    Published on:

  9. The petal senescence of ethylene insensitive species has not been investigated thoroughly while little is known about the temporal and tissue specific expression patterns of transcription factors (TFs) in this...

    Authors: Georgios F Tsanakas, Maria E Manioudaki, Athanasios S Economou and Panagiotis Kalaitzis

    Citation: BMC Genomics 2014 15:554

    Content type: Research article

    Published on:

  10. Picea likiangensis var. balfouriana (Rehd. et Wils.) Hillier ex Slavin (also known as Picea balfouriana) is an ecologically and economically important conifer that grows rapidly under optimum conditions and produ...

    Authors: Qingfen Li, Shougong Zhang and Junhui Wang

    Citation: BMC Genomics 2014 15:553

    Content type: Research article

    Published on:

  11. Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies...

    Authors: Monika Zulawski, Gunnar Schulze, Rostyslav Braginets, Stefanie Hartmann and Waltraud X Schulze

    Citation: BMC Genomics 2014 15:548

    Content type: Research article

    Published on:

  12. Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome ...

    Authors: Nathalia de Setta, Cláudia Barros Monteiro-Vitorello, Cushla Jane Metcalfe, Guilherme Marcelo Queiroga Cruz, Luiz Eduardo Del Bem, Renato Vicentini, Fábio Tebaldi Silveira Nogueira, Roberta Alvares Campos, Sideny Lima Nunes, Paula Cristina Gasperazzo Turrini, Andreia Prata Vieira, Edgar Andrés Ochoa Cruz, Tatiana Caroline Silveira Corrêa, Carlos Takeshi Hotta, Alessandro de Mello Varani, Sonia Vautrin…

    Citation: BMC Genomics 2014 15:540

    Content type: Research article

    Published on:

  13. In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have...

    Authors: Eli Meyer, Michael J Aspinwall, David B Lowry, Juan Diego Palacio-Mejía, Tierney L Logan, Philip A Fay and Thomas E Juenger

    Citation: BMC Genomics 2014 15:527

    Content type: Research article

    Published on:

  14. The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression.

    Authors: Aviv Levy, David Szwerdszarf, Mohamad Abu-Abied, Inna Mordehaev, Yossi Yaniv, Joseph Riov, Tzahi Arazi and Einat Sadot

    Citation: BMC Genomics 2014 15:524

    Content type: Research article

    Published on:

  15. Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the...

    Authors: Guixia Shi, Fang Huang, Yu Gong, Guangli Xu, Jingjing Yu, Zhenbin Hu, Qingsheng Cai and Deyue Yu

    Citation: BMC Genomics 2014 15:510

    Content type: Research article

    Published on:

  16. To combat infection to biotic stress plants elicit the biosynthesis of numerous natural products, many of which are valuable pharmaceutical compounds. Jasmonate is a central regulator of defense response to pa...

    Authors: Craig Schluttenhofer, Sitakanta Pattanaik, Barunava Patra and Ling Yuan

    Citation: BMC Genomics 2014 15:502

    Content type: Research article

    Published on:

  17. Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional ...

    Authors: Berline Fopa Fomeju, Cyril Falentin, Gilles Lassalle, Maria J Manzanares-Dauleux and Régine Delourme

    Citation: BMC Genomics 2014 15:498

    Content type: Research article

    Published on:

  18. In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis c...

    Authors: Yul Ho Kim, Hyang Mi Park, Tae-Young Hwang, Seuk Ki Lee, Man Soo Choi, Sungwoong Jho, Seungwoo Hwang, Hak-Min Kim, Dongwoo Lee, Byoung-Chul Kim, Chang Pyo Hong, Yun Sung Cho, Hyunmin Kim, Kwang Ho Jeong, Min Jung Seo, Hong Tai Yun…

    Citation: BMC Genomics 2014 15:477

    Content type: Methodology article

    Published on:

  19. Poplar seed hair is an environmental annoyance in northern China due to its abundance and widespread airborne distribution after maturation. The morphogenesis and molecular mechanisms of its development are no...

    Authors: Meixia Ye, Zhong Chen, Xiaoxing Su, Lexiang Ji, Jia Wang, Weihua Liao, Huandi Ma and Xinmin An

    Citation: BMC Genomics 2014 15:475

    Content type: Research article

    Published on:

  20. Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in ...

    Authors: Marina de Miguel, José-Antonio Cabezas, Nuria de María, David Sánchez-Gómez, María-Ángeles Guevara, María-Dolores Vélez, Enrique Sáez-Laguna, Luis-Manuel Díaz, Jose-Antonio Mancha, María-Carmen Barbero, Carmen Collada, Carmen Díaz-Sala, Ismael Aranda and María-Teresa Cervera

    Citation: BMC Genomics 2014 15:464

    Content type: Research article

    Published on:

  21. The nonexpressor of pathogenesis-related genes 1, NPR1 (also known as NIM1 and SAI1), is a key regulator of SA-mediated systemic acquired resistance (SAR) in Arabidopsis. In rice, the NPR1 homolog 1 (NH1) interac...

    Authors: Mawsheng Chern, Wei Bai, Deling Ruan, Taeyun Oh, Xuewei Chen and Pamela C Ronald

    Citation: BMC Genomics 2014 15:461

    Content type: Research article

    Published on:

  22. The nature of dynamic traits with their phenotypic plasticity suggests that they are under the control of a dynamic genetic regulation. We employed a precision phenotyping platform to non-invasively assess bio...

    Authors: Wenxin Liu, Manje Gowda, Jochen C Reif, Volker Hahn, Arno Ruckelshausen, Elmar A Weissmann, Hans Peter Maurer and Tobias Würschum

    Citation: BMC Genomics 2014 15:458

    Content type: Research article

    Published on:

  23. Abiotic stresses which include drought and heat are amongst the main limiting factors for plant growth and crop productivity. In the field, these stress types are rarely presented individually and plants are o...

    Authors: Stephanie M Johnson, Fei-Ling Lim, Aliza Finkler, Hillel Fromm, Antoni R Slabas and Marc R Knight

    Citation: BMC Genomics 2014 15:456

    Content type: Research article

    Published on:

  24. Red clover (Trifolium pratense L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important f...

    Authors: Steven A Yates, Martin T Swain, Matthew J Hegarty, Igor Chernukin, Matthew Lowe, Gordon G Allison, Tom Ruttink, Michael T Abberton, Glyn Jenkins and Leif Skøt

    Citation: BMC Genomics 2014 15:453

    Content type: Research article

    Published on:

  25. Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst...

    Authors: Meng Li, Leiting Li, Jim M Dunwell, Xin Qiao, Xing Liu and Shaoling Zhang

    Citation: BMC Genomics 2014 15:444

    Content type: Research article

    Published on:

  26. Small-secreted peptides are emerging as important components in cell-cell communication during basic developmental stages of plant cell growth and development. Plant peptide containing sulfated tyrosine 1 (PSY...

    Authors: Khalid Mahmood, Rubini Kannangara, Kirsten Jørgensen and Anja T Fuglsang

    Citation: BMC Genomics 2014 15:441

    Content type: Research article

    Published on:

  27. Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between seq...

    Authors: Andrey Alexeyenko, Björn Nystedt, Francesco Vezzi, Ellen Sherwood, Rosa Ye, Bjarne Knudsen, Martin Simonsen, Benjamin Turner, Pieter de Jong, Cheng-Cang Wu and Joakim Lundeberg

    Citation: BMC Genomics 2014 15:439

    Content type: Methodology article

    Published on:

  28. Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the...

    Authors: Zongliang Chen, Baobao Wang, Xiaomei Dong, Han Liu, Longhui Ren, Jian Chen, Andrew Hauck, Weibin Song and Jinsheng Lai

    Citation: BMC Genomics 2014 15:433

    Content type: Research article

    Published on:

  29. Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such...

    Authors: Feng Ding, Peng Cui, Zhenyu Wang, Shoudong Zhang, Shahjahan Ali and Liming Xiong

    Citation: BMC Genomics 2014 15:431

    Content type: Research article

    Published on:

  30. Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potent...

    Authors: Ning Guo, Feng Cheng, Jian Wu, Bo Liu, Shuning Zheng, Jianli Liang and Xiaowu Wang

    Citation: BMC Genomics 2014 15:426

    Content type: Research article

    Published on:

  31. Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. The entire cabbage genome sequence and more than fifty thousand proteins have been obtained to date. However a high degree...

    Authors: Senthil Kumar Thamilarasan, Jong-In Park, Hee-Jeong Jung and Ill-Sup Nou

    Citation: BMC Genomics 2014 15:422

    Content type: Research article

    Published on:

  32. Plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. These intricate transcriptional regulatory interactions depend on the recognition...

    Authors: Joel P Tully, Aubrey E Hill, Hadia MR Ahmed, Ryan Whitley, Anthony Skjellum and M Shahid Mukhtar

    Citation: BMC Genomics 2014 15:421

    Content type: Research article

    Published on:

  33. Glandular trichomes are production and storage organs of specialized metabolites such as terpenes, which play a role in the plant’s defense system. The present study aimed to shed light on the regulation of te...

    Authors: Eleni A Spyropoulou, Michel A Haring and Robert C Schuurink

    Citation: BMC Genomics 2014 15:402

    Content type: Research article

    Published on:

  34. Many Poaceae species show a gametophytic self-incompatibility (GSI) system, which is controlled by at least two independent and multiallelic loci, S and Z. Until currently, the gene products for S and Z were unkn...

    Authors: Qingyuan Zhou, Junting Jia, Xing Huang, Xueqing Yan, Liqin Cheng, Shuangyan Chen, Xiaoxia Li, Xianjun Peng and Gongshe Liu

    Citation: BMC Genomics 2014 15:399

    Content type: Research article

    Published on:

  35. Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between y...

    Authors: David D Fang, Johnie N Jenkins, Dewayne D Deng, Jack C McCarty, Ping Li and Jixiang Wu

    Citation: BMC Genomics 2014 15:397

    Content type: Research article

    Published on:

  36. Brassica juncea (AABB) is an allotetraploid species containing genomes of B. rapa (AA) and B. nigra (BB). It is a major oilseed crop in South Asia, and grown on approximately 6–7 million hectares of land in India...

    Authors: Kumar Paritosh, Vibha Gupta, Satish K Yadava, Priyansha Singh, Akshay K Pradhan and Deepak Pental

    Citation: BMC Genomics 2014 15:396

    Content type: Research article

    Published on:

  37. Isatis indigotica Fort. is one of the most commonly used traditional Chinese medicines. Its antiviral compound is a kind of lignan, which is formed with the action of dirigent proteins (DIR). DIR proteins are mem...

    Authors: Qing Li, Junfeng Chen, Ying Xiao, Peng Di, Lei Zhang and Wansheng Chen

    Citation: BMC Genomics 2014 15:388

    Content type: Research article

    Published on:

  38. The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be...

    Authors: Doumit Camilios-Neto, Paloma Bonato, Roseli Wassem, Michelle Z Tadra-Sfeir, Liziane CC Brusamarello-Santos, Glaucio Valdameri, Lucélia Donatti, Helisson Faoro, Vinicius A Weiss, Leda S Chubatsu, Fábio O Pedrosa and Emanuel M Souza

    Citation: BMC Genomics 2014 15:378

    Content type: Research article

    Published on:

  39. Lotus is a diploid plant with agricultural, medicinal, and ecological significance. Genetic linkage maps are fundamental resources for genome and genetic study, and also provide molecular markers for breeding ...

    Authors: Qiong Zhang, Leiting Li, Robert VanBuren, Yanling Liu, Mei Yang, Liming Xu, John E Bowers, Caihong Zhong, Yuepeng Han, Shaohua Li and Ray Ming

    Citation: BMC Genomics 2014 15:372

    Content type: Research article

    Published on:

  40. Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mec...

    Authors: José B Pereira-Leal, Isabel A Abreu, Cláudia S Alabaça, Maria Helena Almeida, Paulo Almeida, Tânia Almeida, Maria Isabel Amorim, Susana Araújo, Herlânder Azevedo, Aleix Badia, Dora Batista, Andreas Bohn, Tiago Capote, Isabel Carrasquinho, Inês Chaves, Ana Cristina Coelho…

    Citation: BMC Genomics 2014 15:371

    Content type: Research article

    Published on:

  41. Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). In recent years, many efforts have been made to construct linkage maps in cu...

    Authors: Xiaojing Zhou, Youlin Xia, Xiaoping Ren, Yulin Chen, Li Huang, Shunmou Huang, Boshou Liao, Yong Lei, Liyin Yan and Huifang Jiang

    Citation: BMC Genomics 2014 15:351

    Content type: Research article

    Published on:

  42. Deep-sequencing has enabled the identification of large numbers of miRNAs and siRNAs, making the high-throughput target identification a main limiting factor in defining their function. In plants, several tool...

    Authors: Prashant K Srivastava, Taraka Ramji Moturu, Priyanka Pandey, Ian T Baldwin and Shree P Pandey

    Citation: BMC Genomics 2014 15:348

    Content type: Research article

    Published on:

  43. High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throug...

    Authors: Jun-ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Kato, Toshio Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hisatoshi Ohta, Hideo Maeda, Kaworu Ebana and Masahiro Yano

    Citation: BMC Genomics 2014 15:346

    Content type: Research article

    Published on:

  44. Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps h...

    Authors: Yongfei Wang, Shoukai Lin, Qi Song, Kuan Li, Huan Tao, Jian Huang, Xinhai Chen, Shufu Que and Huaqin He

    Citation: BMC Genomics 2014 15:344

    Content type: Research article

    Published on:

  45. Bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as Arabidopsis and rice. Little is known about bidirectional gene pairs...

    Authors: Xiaoqing Liu, Xiaojin Zhou, Ye Li, Jian Tian, Qiuxue Zhang, Suzhen Li, Lei Wang, Jun Zhao, Rumei Chen and Yunliu Fan

    Citation: BMC Genomics 2014 15:338

    Content type: Research article

    Published on:

  46. Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P...

    Authors: Jian Zhang, Jianju Feng, Jing Lu, Yongzhi Yang, Xu Zhang, Dongshi Wan and Jianquan Liu

    Citation: BMC Genomics 2014 15:337

    Content type: Research article

    Published on:

  47. Tomato (Solanum lycopersicum), one of the world’s most important vegetable crops, is highly susceptible to necrotrophic fungal pathogens such as Botrytis cinerea and Alternaria solani. Improving resistance throug...

    Authors: Jonathon E Smith, Bemnet Mengesha, Hua Tang, Tesfaye Mengiste and Burton H Bluhm

    Citation: BMC Genomics 2014 15:334

    Content type: Research article

    Published on:

  48. Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signa...

    Authors: Jinhuan Chen, Qianqian Tian, Tao Pang, Libo Jiang, Rongling Wu, Xinli Xia and Weilun Yin

    Citation: BMC Genomics 2014 15:326

    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.