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

    Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.)

    The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well ...

    Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang and Yan Xu

    BMC Genomics 2017 18:744

    Published on: 21 September 2017

  2. Research article

    Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues

    The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to par...

    Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui and Jean-Francois Hausman

    BMC Genomics 2017 18:741

    Published on: 20 September 2017

  3. Research article

    Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana

    During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. This is accompanied by dampened oscillations of circadian clock genes and disrup...

    Majken Pagter, Jessica Alpers, Alexander Erban, Joachim Kopka, Ellen Zuther and Dirk K. Hincha

    BMC Genomics 2017 18:731

    Published on: 16 September 2017

  4. Research article

    Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico

    Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and...

    Matthew A. Kost, Hugo R. Perales, Saranga Wijeratne, Asela J. Wijeratne, Eric Stockinger and Kristin L. Mercer

    BMC Genomics 2017 18:707

    Published on: 8 September 2017

  5. Research article

    Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense

    How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple a...

    Peng-tao Li, Mi Wang, Quan-wei Lu, Qun Ge, Md. Harun or Rashid, Ai-ying Liu, Ju-wu Gong, Hai-hong Shang, Wan-kui Gong, Jun-wen Li, Wei-wu Song, Li-xue Guo, Wei Su, Shao-qi Li, Xiao-ping Guo, Yu-zhen Shi…

    BMC Genomics 2017 18:705

    Published on: 8 September 2017

  6. Research article

    Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato

    Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important...

    Khadiza Khatun, Ujjal Kumar Nath, Arif Hasan Khan Robin, Jong-In Park, Do-Jin Lee, Min-Bae Kim, Chang Kil Kim, Ki-Byung Lim, Ill Sup Nou and Mi-Young Chung

    BMC Genomics 2017 18:695

    Published on: 6 September 2017

  7. Research article

    Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize

    Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tr...

    Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu and Yanli Lu

    BMC Genomics 2017 18:702

    Published on: 6 September 2017

  8. Research article

    Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing

    Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowl...

    Tifu Zhang, Minfeng Gu, Yuhe Liu, Yuanda Lv, Ling Zhou, Haiyan Lu, Shuaiqiang Liang, Huabin Bao and Han Zhao

    BMC Genomics 2017 18:685

    Published on: 5 September 2017

  9. Research article

    Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagat...

    Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori and Akemi Ohmiya

    BMC Genomics 2017 18:683

    Published on: 4 September 2017

  10. Research article

    Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L)

    Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant ...

    Yunlei Zhao, Hongmei Wang, Wei Chen, Pei Zhao, Haiyan Gong, Xiaohui Sang and Yanli Cui

    BMC Genomics 2017 18:661

    Published on: 25 August 2017

  11. Research article

    MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing

    Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Cit...

    Wei-Wei Liang, Jing-Hao Huang, Chun-Ping Li, Lin-Tong Yang, Xin Ye, Dan Lin and Li-Song Chen

    BMC Genomics 2017 18:657

    Published on: 24 August 2017

  12. Research article

    Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86

    Rice (Oryza sativa) is critical for human nutrition worldwide. Due to a growing population, cultivars that produce high yields in high salinity soil are of major importance. Here we describe the discovery and mol...

    Risheng Chen, Yunfeng Cheng, Suying Han, Ben Van Handel, Ling Dong, Xinmin Li and Xiaoqing Xie

    BMC Genomics 2017 18:655

    Published on: 23 August 2017

  13. Research article

    Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

    Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can...

    Keisha D. Carlson, Noe Fernandez-Pozo, Aureliano Bombarely, Rahul Pisupati, Lukas A. Mueller and Andreas Madlung

    BMC Genomics 2017 18:653

    Published on: 23 August 2017

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