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Plant genomics

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 10 of 38

  1. 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

    Content type: Research article

    Published on:

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

  2. 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

    Content type: Methodology article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increas...

    Authors: Xiao-Qing Huang, Xiao-Hong Lu, Man-Hong Sun, Rong-Jun Guo, Anne D. van Diepeningen and Shi-Dong Li

    Citation: BMC Genomics 2019 20:570

    Content type: Research article

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  6. The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube (Ziziphus juju...

    Authors: Hongtai Li, Weilin Gao, Chaoling Xue, Yao Zhang, Zhiguo Liu, Yu Zhang, Xianwei Meng, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:568

    Content type: Research article

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  7. Anthocyanins perform diverse biological functions in plants and are beneficial to human health. Leaf color is the most important trait of ornamental kale and the characteristics of changes in leaf color make i...

    Authors: Ning Guo, Shuo Han, Mei Zong, Guixiang Wang, Shuning Zheng and Fan Liu

    Citation: BMC Genomics 2019 20:564

    Content type: Research article

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  8. Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size ...

    Authors: Marco Meola, Etienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud and Christophe Chassard

    Citation: BMC Genomics 2019 20:560

    Content type: Research article

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  9. Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing...

    Authors: Huiru Sun, Hengling Wei, Hantao Wang, Pengbo Hao, Lijiao Gu, Guoyuan Liu, Liang Ma, Zhengzheng Su and Shuxun Yu

    Citation: BMC Genomics 2019 20:558

    Content type: Research article

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  10. SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family...

    Authors: Hongfeng Wang, Zhichao Lu, Yiteng Xu, Lingcui Kong, Jianjun Shi, Yafei Liu, Chunxiang Fu, Xiaoshan Wang, Zeng-Yu Wang, Chuanen Zhou and Lu Han

    Citation: BMC Genomics 2019 20:552

    Content type: Research article

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  11. Viruses have evolved to create a cellular environment permissive for viral replication in susceptible hosts. Possibly both enabling and resulting from these virus-triggered changes, infected hosts undergo a dr...

    Authors: Mengshi Wu, Xue Ding, Xing Fu and Rosa Lozano-Duran

    Citation: BMC Genomics 2019 20:542

    Content type: Research article

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  12. Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. T...

    Authors: Weixi Li, Dayong Zhang, Guozhong Zhu, Xinyue Mi and Wangzhen Guo

    Citation: BMC Genomics 2019 20:538

    Content type: Research article

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  13. Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and a...

    Authors: Yong Huang, Ling Jiang, Bo-Yu Liu, Cheng-Fang Tan, Dong-Hong Chen, Wen-Hui Shen and Ying Ruan

    Citation: BMC Genomics 2019 20:533

    Content type: Research article

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  14. MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for...

    Authors: Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, Mohcen Benmounah and Hélène Touzet

    Citation: BMC Genomics 2019 20:532

    Content type: Software

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  15. Breeding programs benefit from information about marker-trait associations for many traits, whether the goal is to place those traits under active selection or to maintain them through background selection. As...

    Authors: Teshale Assefa, Paul I. Otyama, Anne V. Brown, Scott R. Kalberer, Roshan S. Kulkarni and Steven B. Cannon

    Citation: BMC Genomics 2019 20:527

    Content type: Research article

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  16. Flavescence dorée is the most serious grapevine yellows disease in Europe. It is caused by phytoplasmas which are transmitted from grapevine to grapevine by the leafhopper Scaphoideus titanus. Differences in susc...

    Authors: Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli and Elisa Angelini

    Citation: BMC Genomics 2019 20:526

    Content type: Research article

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  17. Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng

    Citation: BMC Genomics 2019 20:519

    Content type: Research article

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  18. Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan

    Citation: BMC Genomics 2019 20:514

    Content type: Research article

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  19. DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modificatio...

    Authors: Mei-Wei Luan, Wei Chen, Jian-Feng Xing, Chuan-Le Xiao, Ying Chen and Shang-Qian Xie

    Citation: BMC Genomics 2019 20:508

    Content type: Research article

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  20. Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in see...

    Authors: Xi Zhang, Aiman Hina, Shiyu Song, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao

    Citation: BMC Genomics 2019 20:499

    Content type: Research article

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  21. The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultiva...

    Authors: Yasmin A. Mohamoud, Lisa S. Mathew, Maria F. Torres, Shameem Younuskunju, Robert Krueger, Karsten Suhre and Joel A. Malek

    Citation: BMC Genomics 2019 20:498

    Content type: Research article

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  22. Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance l...

    Authors: Shyam Solanki, Jonathan Richards, Gazala Ameen, Xue Wang, Atiya Khan, Harris Ali, Alex Stangel, Prabin Tamang, Thomas Gross, Patrick Gross, Thomas G. Fetch and Robert S. Brueggeman

    Citation: BMC Genomics 2019 20:495

    Content type: Research article

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  23. Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively...

    Authors: Muhammad Arslan, Upendra Kumar Devisetty, Martin Porsch, Ivo Große, Jochen A. Müller and Stefan G. Michalski

    Citation: BMC Genomics 2019 20:489

    Content type: Research article

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  24. With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post...

    Authors: Sridhar Ravichandran, Raja Ragupathy, Tara Edwards, Michael Domaratzki and Sylvie Cloutier

    Citation: BMC Genomics 2019 20:488

    Content type: Research article

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  25. Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested t...

    Authors: Juan Pablo A. Ortiz, Olivier Leblanc, Cristian Rohr, Mauricio Grisolia, Lorena A. Siena, Maricel Podio, Carolina Colono, Celeste Azzaro and Silvina C. Pessino

    Citation: BMC Genomics 2019 20:487

    Content type: Research article

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  26. In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein,...

    Authors: Moyang Liu, Yongdi Wen, Wenjun Sun, Zhaotang Ma, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2019 20:483

    Content type: Research article

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  27. Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To ...

    Authors: Paul I. Otyama, Andrew Wilkey, Roshan Kulkarni, Teshale Assefa, Ye Chu, Josh Clevenger, Dan J. O’Connor, Graeme C. Wright, Stanley W. Dezern, Gregory E. MacDonald, Noelle L. Anglin, Ethalinda K. S. Cannon, Peggy Ozias-Akins and Steven B. Cannon

    Citation: BMC Genomics 2019 20:481

    Content type: Research article

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  28. The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber c...

    Authors: Yanzhou Wang, Zheng Zeng, Fu Li, Xiufeng Yang, Xinyue Gao, Yonghong Ma, Jing Rao, Hengyun Wang and Touming Liu

    Citation: BMC Genomics 2019 20:476

    Content type: Research article

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  29. Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control th...

    Authors: Emmanuel Avila de Dios, Luis Delaye and June Simpson

    Citation: BMC Genomics 2019 20:473

    Content type: Research article

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  30. Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from ...

    Authors: Sushil Raj Subedi, Nitika Sandhu, Vikas Kumar Singh, Pallavi Sinha, Santosh Kumar, S. P. Singh, Surya Kant Ghimire, Madhav Pandey, Ram Baran Yadaw, Rajeev K. Varshney and Arvind Kumar

    Citation: BMC Genomics 2019 20:471

    Content type: Research article

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  31. The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese juj...

    Authors: Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Hu Fang, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:464

    Content type: Research article

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  32. Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. Elucidating the genetic basis of the biosynthesis of active a...

    Authors: Haiying Ren, Haiyan Yu, Shuwen Zhang, Senmiao Liang, Xiliang Zheng, Shujian Zhang, Pu Yao, Hongkun Zheng and Xingjiang Qi

    Citation: BMC Genomics 2019 20:458

    Content type: Research article

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  33. Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis...

    Authors: Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xingchu Yan and Xinxin Geng

    Citation: BMC Genomics 2019 20:456

    Content type: Research article

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  34. Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is nat...

    Authors: Camila Campos Mantello, Lucas Boatwright, Carla Cristina da Silva, Erivaldo Jose Scaloppi Jr, Paulo de Souza Goncalves, W. Brad Barbazuk and Anete Pereira de Souza

    Citation: BMC Genomics 2019 20:455

    Content type: Research article

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  35. The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although a...

    Authors: Maria José Gonzalo, Aurora Díaz, Narinder P. S. Dhillon, Umesh K. Reddy, Belén Picó and Antonio J. Monforte

    Citation: BMC Genomics 2019 20:448

    Content type: Research article

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  36. Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred g...

    Authors: Qingchun Pan, Junfeng Wei, Feng Guo, Suiyong Huang, Yong Gong, Hao Liu, Jianxiao Liu and Lin Li

    Citation: BMC Genomics 2019 20:443

    Content type: Database

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  37. For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have...

    Authors: Shuantao Liu, Ronghua Wang, Zhigang Zhang, Qiaoyun Li, Lihua Wang, Yongqiang Wang and Zhizhong Zhao

    Citation: BMC Genomics 2019 20:437

    Content type: Research article

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  38. Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. Micro...

    Authors: Tianlun Zhao, Xiaojian Xu, Min Wang, Cheng Li, Cong Li, Rubing Zhao, Shuijin Zhu, Qiuling He and Jinhong Chen

    Citation: BMC Genomics 2019 20:421

    Content type: Research article

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  39. The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subse...

    Authors: Elizabeth A. Cooper, Zachary W. Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris…

    Citation: BMC Genomics 2019 20:420

    Content type: Research article

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  40. Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis...

    Authors: Xinshan Zang, Xiaoli Geng, Lei Ma, Nuohan Wang, Wenfeng Pei, Man Wu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2019 20:402

    Content type: Research article

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  41. Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortio...

    Authors: Hua Chen, Qiang Yang, Kun Chen, Shanshan Zhao, Chong Zhang, Ronglong Pan, Tiecheng Cai, Ye Deng, Xingjun Wang, Yuting Chen, Wenting Chu, Wenping Xie and Weijian Zhuang

    Citation: BMC Genomics 2019 20:392

    Content type: Research article

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  42. Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have bee...

    Authors: Peng-Fei Qi, Yun-Feng Jiang, Zhen-Ru Guo, Qing Chen, Thérèse Ouellet, Lu-Juan Zong, Zhen-Zhen Wei, Yan Wang, Ya-Zhou Zhang, Bin-Jie Xu, Li Kong, Mei Deng, Ji-Rui Wang, Guo-Yue Chen, Qian-Tao Jiang, Xiu-Jin Lan…

    Citation: BMC Genomics 2019 20:390

    Content type: Research article

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  43. Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from ...

    Authors: Le Xue, Zilong He, Xiaochun Bi, Wei Xu, Ting Wei, Shuangxiu Wu and Songnian Hu

    Citation: BMC Genomics 2019 20:383

    Content type: Research article

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  44. Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a ...

    Authors: Mor Rubinstein, Ravit Eshed, Ada Rozen, Tali Zviran, David N. Kuhn, Vered Irihimovitch, Amir Sherman and Ron Ophir

    Citation: BMC Genomics 2019 20:379

    Content type: Research article

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  45. Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate int...

    Authors: Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramirez, Roberto Vera Alvarez, David Landsman and Leonardo Mariño-Ramírez

    Citation: BMC Genomics 2019 20:378

    Content type: Research article

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  46. Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, suc...

    Authors: Guojun Li, Menglu Hou, Yaxue Liu, Yue Pei, Minghui Ye, Yao Zhou, Chenxi Huang, Yaqi Zhao and Haoli Ma

    Citation: BMC Genomics 2019 20:375

    Content type: Research article

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  47. Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering ro...

    Authors: Sovanna Tan, Frédéric Debellé, Pascal Gamas, Florian Frugier and Mathias Brault

    Citation: BMC Genomics 2019 20:373

    Content type: Research article

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  48. Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 f...

    Authors: Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang and Honghao Lv

    Citation: BMC Genomics 2019 20:369

    Content type: Research article

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  49. Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids ...

    Authors: Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk and Zbigniew Zwierzykowski

    Citation: BMC Genomics 2019 20:367

    Content type: Research article

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