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.

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  1. Research article

    Herboxidiene triggers splicing repression and abiotic stress responses in plants

    Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, develop...

    Sahar AlShareef, Yu Ling, Haroon Butt, Kiruthiga G. Mariappan, Moussa Benhamed and Magdy M. Mahfouz

    BMC Genomics 2017 18:260

    Published on: 27 March 2017

  2. Research article

    Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

    Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diver...

    Peng Zhou, Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge and Nevin D. Young

    BMC Genomics 2017 18:261

    Published on: 27 March 2017

  3. Research article

    Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq

    Cotton (Gossypium spp.), as the world’s most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for...

    Chao Shen, Xin Jin, De Zhu and Zhongxu Lin

    BMC Genomics 2017 18:247

    Published on: 23 March 2017

  4. Research article

    Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity

    Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for ...

    Mahmoud W. Yaish, Himanshu V. Patankar, Dekoum V. M. Assaha, Yun Zheng, Rashid Al-Yahyai and Ramanjulu Sunkar

    BMC Genomics 2017 18:246

    Published on: 22 March 2017

  5. Research article

    Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala)

    Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple ...

    Xiao-ping Liu, Bao-zhen Gao, Feng-qing Han, Zhi-yuan Fang, Li-mei Yang, Mu Zhuang, Hong-hao Lv, Yu-mei Liu, Zhan-sheng Li, Cheng-cheng Cai, Hai-long Yu, Zhi-yuan Li and Yang-yong Zhang

    BMC Genomics 2017 18:230

    Published on: 14 March 2017

  6. Research article

    Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

    B. napus (oilseed) is an important source of edible vegetable oil, and its nutritional and economic value is determined by its fatty acid composition and content.

    Cunmin Qu, Ledong Jia, Fuyou Fu, Huiyan Zhao, Kun Lu, Lijuan Wei, Xinfu Xu, Ying Liang, Shimeng Li, Rui Wang and Jiana Li

    BMC Genomics 2017 18:232

    Published on: 14 March 2017

  7. Research article

    The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

    The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the devel...

    Ignazio Verde, Jerry Jenkins, Luca Dondini, Sabrina Micali, Giulia Pagliarani, Elisa Vendramin, Roberta Paris, Valeria Aramini, Laura Gazza, Laura Rossini, Daniele Bassi, Michela Troggio, Shengqiang Shu, Jane Grimwood, Stefano Tartarini, Maria Teresa Dettori…

    BMC Genomics 2017 18:225

    Published on: 11 March 2017

  8. Research article

    Analysis of triglyceride synthesis unveils a green algal soluble diacylglycerol acyltransferase and provides clues to potential enzymatic components of the chloroplast pathway

    Microalgal triglyceride (TAG) synthesis has attracted considerable attention. Particular emphasis has been put towards characterizing the algal homologs of the canonical rate-limiting enzymes, diacylglycerol a...

    Carolina Bagnato, María B. Prados, Gisela R. Franchini, Natalia Scaglia, Silvia E. Miranda and María V. Beligni

    BMC Genomics 2017 18:223

    Published on: 9 March 2017

  9. Research article

    De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes

    The decision for a bud to grow into a branch is a key regulatory process affecting plant architecture. In order to study molecular processes regulating axillary bud outgrowth in the model plant garden pea (Pisum ...

    Stephanie C. Kerr, Federico Gaiti, Christine A. Beveridge and Milos Tanurdzic

    BMC Genomics 2017 18:221

    Published on: 2 March 2017

  10. Research article

    Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development

    As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small no...

    Chao Gao, Pengfei Wang, Shuzhen Zhao, Chuanzhi Zhao, Han Xia, Lei Hou, Zheng Ju, Ye Zhang, Changsheng Li and Xingjun Wang

    BMC Genomics 2017 18:220

    Published on: 2 March 2017

  11. Research article

    A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality

    Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the mos...

    Nuohan Wang, Jianjiang Ma, Wenfeng Pei, Man Wu, Haijing Li, Xingli Li, Shuxun Yu, Jinfa Zhang and Jiwen Yu

    BMC Genomics 2017 18:218

    Published on: 1 March 2017

  12. Research article

    Response of microRNAs to cold treatment in the young spikes of common wheat

    MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, espec...

    Guoqi Song, Rongzhi Zhang, Shujuan Zhang, Yulian Li, Jie Gao, Xiaodong Han, Mingli Chen, Jiao Wang, Wei Li and Genying Li

    BMC Genomics 2017 18:212

    Published on: 28 February 2017

  13. Research article

    Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

    Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure ...

    Jiaming Chen, Xiaoqiang Yang, Xiaomao Huang, Shihua Duan, Chuan Long, Jiakuan Chen and Jun Rong

    BMC Genomics 2017 18:211

    Published on: 28 February 2017

  14. Research article

    Transcriptome of the floral transition in Rosa chinensis ‘Old Blush’

    The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis ‘Ol...

    Xuelian Guo, Chao Yu, Le Luo, Huihua Wan, Ni Zhen, Tingliang Xu, Jiongrui Tan, Huitang Pan and Qixiang Zhang

    BMC Genomics 2017 18:199

    Published on: 23 February 2017

  15. Research article

    Evolution and expression of the fructokinase gene family in Saccharum

    Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasi...

    Yihong Chen, Qing Zhang, Weichang Hu, Xingtan Zhang, Liming Wang, Xiuting Hua, Qingyi Yu, Ray Ming and Jisen Zhang

    BMC Genomics 2017 18:197

    Published on: 21 February 2017

  16. Research article

    Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes

    Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought an...

    Wai Kuan Ho, Hui Hui Chai, Presidor Kendabie, Nariman Salih Ahmad, Jaeyres Jani, Festo Massawe, Andrzej Kilian and Sean Mayes

    BMC Genomics 2017 18:192

    Published on: 20 February 2017

  17. Research article

    Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

    Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in...

    Ana Margarida Ferro, Patrícia Ramos, Olinda Guerreiro, Eliana Jerónimo, Inês Pires, Carmen Capel, Juan Capel, Rafael Lozano, Maria F. Duarte, M. Margarida Oliveira and Sónia Gonçalves

    BMC Genomics 2017 18:183

    Published on: 17 February 2017

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