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

    A reference floral transcriptome of sexual and apomictic Paspalum notatum

    Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associa...

    Juan Pablo A. Ortiz, Santiago Revale, Lorena A. Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc and Silvina C. Pessino

    BMC Genomics 2017 18:318

    Published on: 21 April 2017

  2. Research article

    Global analysis of protein lysine succinylation profiles in common wheat

    Protein lysine succinylation is an important post-translational modification and plays a critical regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Common wheat is ...

    Yumei Zhang, Guangyuan Wang, Limin Song, Ping Mu, Shu Wang, Wenxing Liang and Qi Lin

    BMC Genomics 2017 18:309

    Published on: 20 April 2017

  3. Research article

    Genetics and mapping of a new anthracnose resistance locus in Andean common bean Paloma

    The Andean cultivar Paloma is resistant to Mesoamerican and Andean races of Colletotrichum lindemuthianum, the fungal pathogen that causes the destructive anthracnose disease in common bean. Remarkably, Paloma is...

    Sandra Aparecida de Lima Castro, Maria Celeste Gonçalves-Vidigal, Thiago Alexandre Santana Gilio, Giselly Figueiredo Lacanallo, Giseli Valentini, Vanusa da Silva Ramos Martins, Qijian Song, Marta Zulema Galván, Oscar P. Hurtado-Gonzales and Marcial Antonio Pastor-Corrales

    BMC Genomics 2017 18:306

    Published on: 18 April 2017

  4. Research article

    Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

    DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown.

    Xuke Lu, Xiaoge Wang, Xiugui Chen, Na Shu, Junjuan Wang, Delong Wang, Shuai Wang, Weili Fan, Lixue Guo, Xiaoning Guo and Wuwei Ye

    BMC Genomics 2017 18:297

    Published on: 13 April 2017

  5. Research article

    QTL mapping for fruit quality in Citrus using DArTseq markers

    Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arr...

    Maiara Curtolo, Mariângela Cristofani-Yaly, Rodrigo Gazaffi, Marco Aurélio Takita, Antonio Figueira and Marcos Antonio Machado

    BMC Genomics 2017 18:289

    Published on: 12 April 2017

  6. Research article

    Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining ...

    William B. Rutter, Andres Salcedo, Alina Akhunova, Fei He, Shichen Wang, Hanquan Liang, Robert L. Bowden and Eduard Akhunov

    BMC Genomics 2017 18:291

    Published on: 12 April 2017

  7. Research article

    Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

    Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimond...

    Liuxin Xiang, Jinggao Liu, Chaofeng Wu, Yushan Deng, Chaowei Cai, Xiao Zhang and Yingfan Cai

    BMC Genomics 2017 18:292

    Published on: 12 April 2017

  8. Research article

    Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway

    The accumulation of anthocyanin in horticultural crops not only improves their stress tolerances but also their nutritional values. Many key regulatory and structural genes in anthocyanin biosynthesis have bee...

    Lu Zhang, Bin Xu, Tao Wu, Yanfang Yang, Lianxue Fan, Muxuan Wen and Jiaxin Sui

    BMC Genomics 2017 18:288

    Published on: 11 April 2017

  9. Research article

    Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

    Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall...

    Antanas V. Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller and Andrew Merchant

    BMC Genomics 2017 18:284

    Published on: 7 April 2017

  10. Research article

    Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq)

    Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mech...

    Wei Qian, Guiyan Fan, Dandan Liu, Helong Zhang, Xiaowu Wang, Jian Wu and Zhaosheng Xu

    BMC Genomics 2017 18:276

    Published on: 4 April 2017

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

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