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

    Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

    Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mec...

    Lei Wang, Hong-Ling Wang, Lan Yin and Chang-Yan Tian

    BMC Genomics 2017 18:806

    Published on: 19 October 2017

  2. Research article

    Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

    Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and applicat...

    Jin Xiao, Keli Dai, Lian Fu, Jan Vrána, Marie Kubaláková, Wentao Wan, Haojie Sun, Jing Zhao, Chunyan Yu, Yufeng Wu, Michael Abrouk, Haiyan Wang, Jaroslav Doležel and Xiue Wang

    BMC Genomics 2017 18:791

    Published on: 16 October 2017

  3. Research article

    miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri

    Sterile and fertile flowers are important evolutionary developmental phenotypes in angiosperm flowers. The development of floral organs, critical in angiosperm reproduction, is regulated by microRNAs (miRNAs)....

    Weixing Li, Zhichong He, Li Zhang, Zhaogeng Lu, Jing Xu, Jiawen Cui, Li Wang and Biao Jin

    BMC Genomics 2017 18:783

    Published on: 13 October 2017

  4. Research article

    Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice

    The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin ...

    Xiucai Pan, Yuan Fang, Xueming Yang, Dongyang Zheng, Lifen Chen, Lei Wang, Jin Xiao, Xiu-e Wang, Kai Wang, Zhukuan Cheng, Hengxiu Yu and Wenli Zhang

    BMC Genomics 2017 18:778

    Published on: 12 October 2017

  5. Research article

    Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers

    Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population struct...

    Berhanu Tadesse Ertiro, Kassa Semagn, Biswanath Das, Michael Olsen, Maryke Labuschagne, Mosisa Worku, Dagne Wegary, Girum Azmach, Veronica Ogugo, Tolera Keno, Beyene Abebe, Temesgen Chibsa and Abebe Menkir

    BMC Genomics 2017 18:777

    Published on: 12 October 2017

  6. Research article

    Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

    After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domesticat...

    Roland Akakpo, Nora Scarcelli, Hana Chaïr, Alexandre Dansi, Gustave Djedatin, Anne-Céline Thuillet, Bénédicte Rhoné, Olivier François, Karine Alix and Yves Vigouroux

    BMC Genomics 2017 18:782

    Published on: 12 October 2017

  7. Research article

    Genes for asparagine metabolism in Lotus japonicus: differential expression and interconnection with photorespiration

    Asparagine is a very important nitrogen transport and storage compound in plants due to its high nitrogen/carbon ratio and stability. Asparagine intracellular concentration depends on a balance between asparag...

    Margarita García-Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, José M. Vega, Marco Betti and Antonio J. Márquez

    BMC Genomics 2017 18:781

    Published on: 12 October 2017

  8. Research article

    Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus

    Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from div...

    Nadia Raboanatahiry, Hongbo Chao, Liangxing Guo, Jianping Gan, Jun Xiang, Mingli Yan, Libin Zhang, Longjiang Yu and Maoteng Li

    BMC Genomics 2017 18:776

    Published on: 12 October 2017

  9. Research article

    Cell wall metabolism and hexose allocation contribute to biomass accumulation in high yielding extreme segregants of a Saccharum interspecific F2 population

    Sugarcane is an emerging dual-purpose biofuel crop for energy and sugar production, owing to its rapid growth rate, high sucrose storage in the stems, and high lignocellulosic yield. It has the highest biomass...

    Ching Man Wai, Jisen Zhang, Tyler C. Jones, Chifumi Nagai and Ray Ming

    BMC Genomics 2017 18:773

    Published on: 11 October 2017

  10. Research article

    Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance

    The harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a go...

    Junjun Liang, Xin Chen, Guangbing Deng, Zhifen Pan, Haili Zhang, Qiao Li, Kaijun Yang, Hai Long and Maoqun Yu

    BMC Genomics 2017 18:775

    Published on: 11 October 2017

  11. Research article

    The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat

    Wheat is one of the three major cereals that have been domesticated to feed human populations. The composition of the wheat grain determines the functional properties of wheat including milling efficiency, bre...

    Parimalan Rangan, Agnelo Furtado and Robert J. Henry

    BMC Genomics 2017 18:766

    Published on: 11 October 2017

  12. Research article

    Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane

    Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases in the sugarcane industry. Using a molecular biological technique to mine sugarcane resistance genes can provide gene res...

    Feng Liu, Tingting Sun, Ling Wang, Weihua Su, Shiwu Gao, Yachun Su, Liping Xu and Youxiong Que

    BMC Genomics 2017 18:771

    Published on: 11 October 2017

  13. Research article

    Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana

    Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regul...

    Xiao-Ning Zhang, Yifei Shi, Jordan J. Powers, Nikhil B. Gowda, Chong Zhang, Heba M. M. Ibrahim, Hannah B. Ball, Samuel L. Chen, Hua Lu and Stephen M. Mount

    BMC Genomics 2017 18:772

    Published on: 11 October 2017

  14. Research Article

    Genome-wide analysis of rice cis-natural antisense transcription under cadmium exposure using strand-specific RNA-Seq

    The elucidation of novel transcripts and their expression in response to various stress conditions is necessary to understand the transcriptional network of plants as an adaptation to biotic and abiotic stress...

    Youko Oono, Takayuki Yazawa, Hiroyuki Kanamori, Harumi Sasaki, Satomi Mori and Takashi Matsumoto

    BMC Genomics 2017 18:761

    Published on: 6 October 2017

  15. Research article

    Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)

    Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainl...

    Ming Li, Zhaoxu Liang, Shanshan He, Yuan Zeng, Yan Jing, Weikuan Fang, Kaichao Wu, Guanyu Wang, Xia Ning, Lunwang Wang, Song Li, Hongwei Tan and Fang Tan

    BMC Genomics 2017 18:754

    Published on: 25 September 2017

  16. 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

  17. 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

  18. 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

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