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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 1 of 30

  1. Content type: Research article

    Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been con...

    Authors: Licao Cui, Guang Yang, Jiali Yan, Yan Pan and Xiaojun Nie

    Citation: BMC Genomics 2019 20:750

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  2. Content type: Research article

    The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehe...

    Authors: Mengyuan Wei, Aili Liu, Yujuan Zhang, Yong Zhou, Donghua Li, Komivi Dossa, Rong Zhou, Xiurong Zhang and Jun You

    Citation: BMC Genomics 2019 20:748

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  3. Content type: Research article

    Gibberellins (GAs) can have profound effects on growth and development in higher plants. In contrast to their flowering-promotive role in many well-studied plants, GAs can repress flowering in woody perennial ...

    Authors: Songwen Zhang, Christopher Gottschalk and Steve van Nocker

    Citation: BMC Genomics 2019 20:747

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  4. Content type: Research article

    High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Under...

    Authors: Pietro Delfino, Sara Zenoni, Zahra Imanifard, Giovanni Battista Tornielli and Diana Bellin

    Citation: BMC Genomics 2019 20:739

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  5. Content type: Research article

    ERECTA (ER) is a leucine-rich repeat-receptor-like kinase gene (LRR-RLK) encoding a protein isolated from Arabidopsis. Although the regulatory functions of ER genes have been widely explored in plant development ...

    Authors: Hanshuai Li, Xiaodong Han, Xinxiang Liu, Miaoyi Zhou, Wen Ren, Bingbing Zhao, Chuanli Ju, Ya Liu and Jiuran Zhao

    Citation: BMC Genomics 2019 20:737

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  6. Content type: Research article

    Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators,...

    Authors: Rui Chen, Ming Li, Huiyuan Zhang, Lijin Duan, Xianjun Sun, Qiyan Jiang, Hui Zhang and Zheng Hu

    Citation: BMC Genomics 2019 20:730

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  7. Content type: Research article

    Clerodendrum inerme (L.) Gaertn, a halophyte, usually grows on coastal beaches as an important mangrove plant. The salt-tolerant mechanisms and related genes of this species that respond to short-term salinity st...

    Authors: Yuping Xiong, Haifeng Yan, Hanzhi Liang, Yueya Zhang, Beiyi Guo, Meiyun Niu, Shuguang Jian, Hai Ren, Xinhua Zhang, Yuan Li, Songjun Zeng, Kunlin Wu, Feng Zheng, Jaime A. Teixeira da Silva and Guohua Ma

    Citation: BMC Genomics 2019 20:724

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  8. Content type: Research article

    Inflorescence dichotomy in Musa species is a rare developmental event which leads to the production of multiple bunches on a single pseudostem at fruiting. In spite of its fascinating attraction and seductive app...

    Authors: Ebiamadon Andi Brisibe and Norah Godwin Ekanem

    Citation: BMC Genomics 2019 20:713

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  9. Content type: Research article

    Candidatus Phytoplasma solani’ is endemic in Europe and infects a wide range of weeds and cultivated plants. Phytoplasmas are prokaryotic plant pathogens that colonize the sieve elements of their host plant, cau...

    Authors: Sara Buoso, Laura Pagliari, Rita Musetti, Marta Martini, Fabio Marroni, Wolfgang Schmidt and Simonetta Santi

    Citation: BMC Genomics 2019 20:703

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  10. Content type: Research article

    The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing...

    Authors: Xing Wu, Christopher Heffelfinger, Hongyu Zhao and Stephen L. Dellaporta

    Citation: BMC Genomics 2019 20:701

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  11. Content type: Research article

    Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinal herb, whose main bioactive constituents are flavonoids. Chilling sensitivity is the dominant environmental factor limiting growth and development of t...

    Authors: Xin Peng, Hao Wu, Hongjiang Chen, Yujiong Zhang, Dan Qiu and Zhongyi Zhang

    Citation: BMC Genomics 2019 20:687

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  12. Content type: Research article

    Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyani...

    Authors: Yongjun He, Hang Chen, Lu Zhou, Yang Liu and Huoying Chen

    Citation: BMC Genomics 2019 20:678

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  13. Content type: Research article

    Herbivorous insects can have a profound impact on plant growth performance. In some years, canopy damage in poplar plantations exceeds 50% of the total leaf surface, thereby possibly compromising carbon fixati...

    Authors: Niels A. Müller, Birgit Kersten, Matthias Fladung and Hilke Schroeder

    Citation: BMC Genomics 2019 20:673

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  14. Content type: Research article

    Ethylene signal transduction in plants is conducted by the two-component system (TCS) which consists of histidine kinase (HK), histidine phosphotransferase (HPT) and response regulators (RRs). This system play...

    Authors: Yogeshwar V. Dhar, Deepika Lakhwani, Ashutosh Pandey, Shikha Singh, Prabodh K. Trivedi and Mehar H. Asif

    Citation: BMC Genomics 2019 20:674

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  15. Content type: Research article

    Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns...

    Authors: Vasudevan Ayyappan, Venkateswara R. Sripathi, Venu ( Kal) Kalavacharla, Malay C. Saha, Jyothi Thimmapuram, Ketaki P. Bhide and Elizabeth Fiedler

    Citation: BMC Genomics 2019 20:667

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  16. Content type: Research article

    Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in L...

    Authors: Haron Salih, Wenfang Gong, Shoupu He, Wang Xia, Magwanga Richard Odongo and Xiongming Du

    Citation: BMC Genomics 2019 20:661

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  17. Content type: Research article

    Wheat is the most important staple crop in Afghanistan and accounts for the main part of cereal production. However, wheat production has been unstable during the last decades and the country depends on seed i...

    Authors: S. Dreisigacker, R. K. Sharma, E. Huttner, A. Karimov, M. Q. Obaidi, P. K. Singh, C. Sansaloni, R. Shrestha, K. Sonder and H.-J. Braun

    Citation: BMC Genomics 2019 20:660

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  18. Content type: Research article

    Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms under...

    Authors: Qi Wu, Xue Bai, Wei Zhao, Xiaodong Shi, Dabing Xiang, Yan Wan, Xiaoyong Wu, Yanxia Sun, Jianglin Zhao, Lianxin Peng and Gang Zhao

    Citation: BMC Genomics 2019 20:658

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  19. Content type: Research article

    Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly...

    Authors: Siyuan Zhu, Xiaojun Chen, Xia Liu, Jian Zhao and Touming Liu

    Citation: BMC Genomics 2019 20:657

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  20. Content type: Research article

    Argonaute proteins (AGOs) are important players in the regulation of plant development by directing sRNAs to target mRNAs. In maize (Zea mays), AGO18b is a tassel-enriched and grass-specific AGO. Previous studies...

    Authors: Wei Sun, Dong Chen, Yaqiang Xue, Lihong Zhai, Dan Zhang, Zheng Cao, Lei Liu, Chao Cheng, Yi Zhang and Zuxin Zhang

    Citation: BMC Genomics 2019 20:656

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  21. Content type: Research article

    Circular RNAs (circRNAs), a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and developmental processes in eukaryotic cells. However, there have been no related stud...

    Authors: Xingguo Zhang, Xingli Ma, Longlong Ning, Zhongfeng Li, Kunkun Zhao, Ke Li, Jialin He and Dongmei Yin

    Citation: BMC Genomics 2019 20:653

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  22. Content type: Research article

    The efficient detection and initiation of appropriate response to abiotic stresses are important to plants survival. The plant G-protein coupled receptors (GPCRs) are diverse membranous proteins that are respo...

    Authors: Pu Lu, Richard Odongo Magwanga, Joy Nyangasi Kirungu, Qi Dong, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, Yanchao Xu, Yuqing Hou, Renhai Peng, Kunbo Wang and Fang Liu

    Citation: BMC Genomics 2019 20:651

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  23. Content type: Research article

    Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped...

    Authors: Shang Gao, Zhi Zheng, Jonathan Powell, Ahsan Habib, Jiri Stiller, Meixue Zhou and Chunji Liu

    Citation: BMC Genomics 2019 20:650

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  24. Content type: Research article

    Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (An...

    Authors: Libin Zhang, Jun Zou, Shisheng Li, Baoshan Wang, Nadia Raboanatahiry and Maoteng Li

    Citation: BMC Genomics 2019 20:649

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  25. Content type: Research article

    The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 1...

    Authors: Xue Zhao, Hairan Dong, Hong Chang, Jingyun Zhao, Weili Teng, Lijuan Qiu, Wenbin Li and Yingpeng Han

    Citation: BMC Genomics 2019 20:648

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  26. Content type: Research article

    The thermo-sensitive genic male sterility (TGMS) of Brassica napus facilitates reproductive researches and hybrid seed production. Considering the complexity and little information about the molecular mechanism i...

    Authors: Xin Tang, You-Jin Hao, Jun-Xing Lu, Geng Lu and Tao Zhang

    Citation: BMC Genomics 2019 20:644

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  27. Content type: Research article

    As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striif...

    Authors: Xueling Ye, Jian Li, Yukun Cheng, Fangjie Yao, Li Long, Yuqi Wang, Yu Wu, Jing Li, Jirui Wang, Qiantao Jiang, Houyang Kang, Wei Li, Pengfei Qi, Xiujin Lan, Jian Ma, Yaxi Liu…

    Citation: BMC Genomics 2019 20:640

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  28. Content type: Research article

    Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. ...

    Authors: Harsh Raman, Rosy Raman, Yu Qiu, Avilash Singh Yadav, Sridevi Sureshkumar, Lauren Borg, Maheswaran Rohan, David Wheeler, Oliver Owen, Ian Menz and Sureshkumar Balasubramanian

    Citation: BMC Genomics 2019 20:636

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  29. Content type: Methodology article

    The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found ...

    Authors: Marc-André Lemay, Davoud Torkamaneh, Guillem Rigaill, Brian Boyle, Adrian O. Stec, Robert M. Stupar and François Belzile

    Citation: BMC Genomics 2019 20:634

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  30. Content type: Research article

    Gypenosides are a group of triterpene saponins from Gynostemma pentaphyllum that are the same as or very similar to ginsenosides from the Panax species. Several enzymes involved in ginsenoside biosynthesis have b...

    Authors: Tongtong Liang, Liqiu Zou, Sijie Sun, Xuejun Kuang, Jianhe Wei, Lizhi Wang, Ying Li and Chao Sun

    Citation: BMC Genomics 2019 20:632

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  31. Content type: Research article

    Free asparagine is the precursor for acrylamide formation during cooking and processing of grains, tubers, beans and other crop products. In wheat grain, free asparagine, free glutamine and total free amino ac...

    Authors: Tanya Y. Curtis, Sarah Raffan, Yongfang Wan, Robert King, Asier Gonzalez-Uriarte and Nigel G. Halford

    Citation: BMC Genomics 2019 20:628

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  32. Content type: Research article

    Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly g...

    Authors: Yeyun Li, Xuewen Wang, Qiuyan Ban, Xiangxiang Zhu, Changjun Jiang, Chaoling Wei and Jeffrey L. Bennetzen

    Citation: BMC Genomics 2019 20:624

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  33. Content type: Research article

    Heavy metal ATPases (HMAs) are responsible for Cd translocation and play a primary role in Cd detoxification in various plant species. However, the characteristics of HMAs and the regulatory mechanisms between...

    Authors: Min Zhou, Shigang Zheng, Rong Liu, Lu Lu, Chihong Zhang, Lei Zhang, Levi Yant and Yu Wu

    Citation: BMC Genomics 2019 20:615

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  34. Content type: Research article

    Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the ...

    Authors: Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra Mathioni, Blake C. Meyers, Dan Nettleton and Roger P. Wise

    Citation: BMC Genomics 2019 20:610

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    The Correction to this article has been published in BMC Genomics 2019 20:697

  35. Content type: Research article

    Quercetin is a polyphenol of great interest given its antioxidant activity and involvement in the immune response. Although quercetin has been well studied at the molecular level as a gene regulator and an act...

    Authors: Dana Atrahimovich, Avraham O. Samson, Yifthah Barsheshet, Jacob Vaya, Soliman Khatib and Eli Reuveni

    Citation: BMC Genomics 2019 20:606

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  36. Content type: Research article

    A thorough verification of the ability of genomic selection (GS) to predict estimated breeding values for pea (Pisum sativum L.) grain yield is pending. Prediction for different environments (inter-environment pr...

    Authors: Paolo Annicchiarico, Nelson Nazzicari, Luciano Pecetti, Massimo Romani and Luigi Russi

    Citation: BMC Genomics 2019 20:603

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  37. Content type: Research article

    Long intergenic non-coding RNAs (lincRNAs) can act as regulators of expression of protein-coding genes. Trans-natural antisense transcripts (trans-NATs) are a type of lincRNAs that contain sequence complementary ...

    Authors: Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon and Yves Poirier

    Citation: BMC Genomics 2019 20:601

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  38. Content type: Research article

    Gerbera hybrida is one of the most popular cut flowers in the world; however, stem bending, which always happens when gerbera flower harvested from the field, greatly limits its vase life. To date the molecular m...

    Authors: Yafei Ge, Qixian Lai, Ping Luo, Xiaojing Liu and Wen Chen

    Citation: BMC Genomics 2019 20:600

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  39. Content type: Research article

    Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quali...

    Authors: Wenwen Wang, Ying Sun, Peng Yang, Xiaoyan Cai, Le Yang, Junrui Ma, Yuncan Ou, Tianpeng Liu, Iftikhar Ali, Dajun Liu, Jian Zhang, Zhonghua Teng, Kai Guo, Dexin Liu, Fang Liu and Zhengsheng Zhang

    Citation: BMC Genomics 2019 20:599

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  40. Content type: Research article

    Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. P...

    Authors: Sony Kumari, Sandeep Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar and Kishore C. S. Panigrahi

    Citation: BMC Genomics 2019 20:596

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  41. Content type: Research article

    The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant’s geno...

    Authors: Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm and Heinz Himmelbauer

    Citation: BMC Genomics 2019 20:594

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  42. Content type: Research article

    Puccinellia tenuiflora is the most saline-alkali tolerant plant in the Songnen Plain, one of the three largest soda saline-alkali lands worldwide. Here, we investigated the physicochemical properties of saline-al...

    Authors: Xiaoxue Ye, Hao Wang, Xiuling Cao, Xuejiao Jin, Fuqiang Cui, Yuanyuan Bu, Hua Liu, Wenwu Wu, Tetsuo Takano and Shenkui Liu

    Citation: BMC Genomics 2019 20:589

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  43. Content type: Research article

    Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food i...

    Authors: Abdul Fatah A. Samad, Reyhaneh Rahnamaie-Tajadod, Muhammad Sajad, Jaeyres Jani, Abdul Munir Abdul Murad, Normah Mohd Noor and Ismanizan Ismail

    Citation: BMC Genomics 2019 20:586

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    The Correction to this article has been published in BMC Genomics 2019 20:627

  44. Content type: Methodology article

    Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequenc...

    Authors: Sean P. Gordon, Joshua J. Levy and John P. Vogel

    Citation: BMC Genomics 2019 20:580

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  45. Content type: Research article

    Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regul...

    Authors: Ge Bai, He Xie, Heng Yao, Feng Li, Xuejun Chen, Yihan Zhang, Bingguan Xiao, Jun Yang, Yongping Li and Da-Hai Yang

    Citation: BMC Genomics 2019 20:575

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  46. Content type: Research article

    Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expressi...

    Authors: Xiaocong Zhang, Sidi Xie, Jienan Han, Yu Zhou, Chang Liu, Zhiqiang Zhou, Feifei Wang, Zixiang Cheng, Junjie Zhang, Yufeng Hu, Zhuanfang Hao, Mingshun Li, Degui Zhang, Hongjun Yong, Yubi Huang, Jianfeng Weng…

    Citation: BMC Genomics 2019 20:574

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