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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 31

  1. Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is ma...

    Authors: Shimin Fu, Jonathan Shao, Avijit Roy, Ronald H. Brlansky, Changyong Zhou and John S. Hartung

    Citation: BMC Genomics 2019 20:969

    Content type: Research article

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  2. Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yell...

    Authors: Daiyan Li, Juwei Zhang, Haijiao Liu, Binwen Tan, Wei Zhu, Lili Xu, Yi Wang, Jian Zeng, Xing Fan, Lina Sha, Haiqin Zhang, Jian Ma, Guoyue Chen, Yonghong Zhou and Houyang Kang

    Citation: BMC Genomics 2019 20:963

    Content type: Research article

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  3. The advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-g...

    Authors: Mao Qin, Shigang Wu, Alun Li, Fengli Zhao, Hu Feng, Lulu Ding and Jue Ruan

    Citation: BMC Genomics 2019 20:955

    Content type: Software

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  4. Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most w...

    Authors: Vanessa Ferreira, José Tomás Matus, Olinda Pinto-Carnide, David Carrasco, Rosa Arroyo-García and Isaura Castro

    Citation: BMC Genomics 2019 20:952

    Content type: Research article

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  5. Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB res...

    Authors: Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David J. Konkin, Ron E. Knox, Yuefeng Ruan and Pierre R. Fobert

    Citation: BMC Genomics 2019 20:925

    Content type: Research article

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  6. GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, indu...

    Authors: Yao Chen, Panpan Zhu, Shaoyuan Wu, Yan Lu, Jian Sun, Qinghe Cao, Zongyun Li and Tao Xu

    Citation: BMC Genomics 2019 20:911

    Content type: Research article

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  7. Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it in...

    Authors: Sapinder Bali, Kelly Vining, Cynthia Gleason, Hassan Majtahedi, Charles R. Brown and Vidyasagar Sathuvalli

    Citation: BMC Genomics 2019 20:907

    Content type: Research article

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  8. The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is t...

    Authors: Rashmi Jain, Jerry Jenkins, Shengqiang Shu, Mawsheng Chern, Joel A. Martin, Dario Copetti, Phat Q. Duong, Nikki T. Pham, David A. Kudrna, Jayson Talag, Wendy S. Schackwitz, Anna M. Lipzen, David Dilworth, Diane Bauer, Jane Grimwood, Catherine R. Nelson…

    Citation: BMC Genomics 2019 20:905

    Content type: Research article

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  9. Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, has been one of the most devastating pathogens affecting soybean production. In the United States alone, SCN damage accounted for more than $1 billion lo...

    Authors: Waltram Second Ravelombola, Jun Qin, Ainong Shi, Liana Nice, Yong Bao, Aaron Lorenz, James H. Orf, Nevin D. Young and Senyu Chen

    Citation: BMC Genomics 2019 20:904

    Content type: Research article

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  10. Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of kno...

    Authors: Vinicius Vilperte, Calin Rares Lucaciu, Heidi Halbwirth, Robert Boehm, Thomas Rattei and Thomas Debener

    Citation: BMC Genomics 2019 20:900

    Content type: Research article

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  11. Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the...

    Authors: Bin Tan, Xiaodong Lian, Jun Cheng, Wenfang Zeng, Xianbo Zheng, Wei Wang, Xia Ye, Jidong Li, Zhiqian Li, Langlang Zhang and Jiancan Feng

    Citation: BMC Genomics 2019 20:892

    Content type: Research article

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  12. Barley yellow dwarf (BYD) is an important virus disease that causes significant reductions in wheat yield. For effective control of Barley yellow dwarf virus through breeding, the identification of genetic source...

    Authors: Shormin Choudhury, Philip Larkin, Rugen Xu, Matthew Hayden, Kerrie Forrest, Holger Meinke, Hongliang Hu, Meixue Zhou and Yun Fan

    Citation: BMC Genomics 2019 20:891

    Content type: Research article

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  13. Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait ...

    Authors: Kuang Zhang, Vasu Kuraparthy, Hui Fang, Linglong Zhu, Shilpa Sood and Don C. Jones

    Citation: BMC Genomics 2019 20:889

    Content type: Research article

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  14. Melatonin is a ubiquitous molecule and exists across kingdoms. Studies on melatonin in plants have mainly focused on its physiological influence on growth and development, and on its biosynthesis. A number of ...

    Authors: Yihe Yu, Lu Bian, Zeling Jiao, Keke Yu, Yutong Wan, Guohai Zhang and Dalong Guo

    Citation: BMC Genomics 2019 20:880

    Content type: Research article

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  15. Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb t...

    Authors: Meng-qi Wang, Zhen-yu Bai, Ya-fang Xiao, Yan Li, Qing-lin Liu, Lei Zhang, Yuan-zhi Pan, Bei-bei Jiang and Fan Zhang

    Citation: BMC Genomics 2019 20:877

    Content type: Research article

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  16. Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supp...

    Authors: Fernando P. Guerra, Haktan Suren, Jason Holliday, James H. Richards, Oliver Fiehn, Randi Famula, Brian J. Stanton, Richard Shuren, Robert Sykes, Mark F. Davis and David B. Neale

    Citation: BMC Genomics 2019 20:875

    Content type: Research article

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  17. Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing num...

    Authors: Kadriye Kahraman and Stuart James Lucas

    Citation: BMC Genomics 2019 20:874

    Content type: Research article

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  18. Heat shock transcription factor (Hsfs) is widely found in eukaryotes and prokaryotes. Hsfs can not only help organisms resist high temperature, but also participate in the regulation of plant growth and develo...

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

    Citation: BMC Genomics 2019 20:871

    Content type: Research article

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  19. Gynostemma pentaphyllum is an important perennial medicinal herb belonging to the family Cucurbitaceae. Aerial stem-to-rhizome transition before entering the winter is an adaptive regenerative strategy in G. pent...

    Authors: Qi Yang, Shibiao Liu, Xiaoning Han, Jingyi Ma, Wenhong Deng, Xiaodong Wang, Huihong Guo and Xinli Xia

    Citation: BMC Genomics 2019 20:865

    Content type: Research article

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  20. Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our ...

    Authors: Yuanda Lv, Fengqin Hu, Yongfeng Zhou, Feilong Wu and Brandon S. Gaut

    Citation: BMC Genomics 2019 20:864

    Content type: Research article

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  21. Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. ...

    Authors: Zongyu Zhang, Wengang Xie, Junchao Zhang, Na Wang, Yongqiang Zhao, Yanrong Wang and Shiqie Bai

    Citation: BMC Genomics 2019 20:861

    Content type: Research article

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  22. Saffron crocus (Crocus sativus) is a valuable spice with medicinal uses in gynaecopathia and nervous system diseases. Identify flowering regulatory genes plays a vital role in increasing flower numbers, thereby r...

    Authors: Xiaodong Qian, Youping Sun, Guifen Zhou, Yumei Yuan, Jing Li, Huilian Huang, Limin Xu and Liqin Li

    Citation: BMC Genomics 2019 20:857

    Content type: Research article

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  23. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their in.....

    Authors: Xi Chen, Shuo Sun, Fangjie Liu, Enhui Shen, Lu Liu, Chuyu Ye, Bingguang Xiao, Michael P. Timko, Qian-Hao Zhu, Longjiang Fan and Peijian Cao

    Citation: BMC Genomics 2019 20:856

    Content type: Research article

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  24. The MinION Access Program (MAP, 2014–2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In ...

    Authors: Thomas Sauvage, William E. Schmidt, Hwan Su Yoon, Valerie J. Paul and Suzanne Fredericq

    Citation: BMC Genomics 2019 20:850

    Content type: Research article

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  25. Insertions/deletions (InDels) and more specifically presence/absence variations (PAVs) are pervasive in several species and have strong functional and phenotypic effect by removing or drastically modifying gen...

    Authors: Clément Mabire, Jorge Duarte, Aude Darracq, Ali Pirani, Hélène Rimbert, Delphine Madur, Valérie Combes, Clémentine Vitte, Sébastien Praud, Nathalie Rivière, Johann Joets, Jean-Philippe Pichon and Stéphane D. Nicolas

    Citation: BMC Genomics 2019 20:848

    Content type: Methodology article

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  26. Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of gene...

    Authors: Hui Song, Zhonglong Guo, Xiaohui Hu, Lang Qian, Fuhong Miao, Xiaojun Zhang and Jing Chen

    Citation: BMC Genomics 2019 20:844

    Content type: Research article

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  27. Intraspecific variations among induced responses might lead to understanding of adaptive variations in defense strategies against insects. We employed RNA-Seq transcriptome screening to elucidate the molecular...

    Authors: Ariel Ogran, Adi Faigenboim and Oz Barazani

    Citation: BMC Genomics 2019 20:843

    Content type: Research article

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  28. Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass found in semi-arid regions that is well adapted for growth in sandy soils and drought conditions. E. curvula constitutes a polymorphic com...

    Authors: Ingrid Garbus, Juan Pablo Selva, María Cielo Pasten, Andrés Martín Bellido, José Carballo, Emidio Albertini and Viviana Echenique

    Citation: BMC Genomics 2019 20:839

    Content type: Research article

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  29. Pachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000 m where it i...

    Authors: Yanni Dong, Saurabh Gupta, Rixta Sievers, Jason J. Wargent, David Wheeler, Joanna Putterill, Richard Macknight, Tsanko Gechev, Bernd Mueller-Roeber and Paul P. Dijkwel

    Citation: BMC Genomics 2019 20:838

    Content type: Research article

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  30. Cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system is an important mechanism to produce F1 hybrid seeds. Understanding the interaction that controls restoration at a molecular level wil...

    Authors: Bingqiang Wei, Lanlan Wang, Paul W. Bosland, Gaoyuan Zhang and Ru Zhang

    Citation: BMC Genomics 2019 20:837

    Content type: Research article

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  31. The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been wel...

    Authors: Soo-Rang Lee, Kyeonghee Kim, Byoung-Yoon Lee and Chae Eun Lim

    Citation: BMC Genomics 2019 20:833

    Content type: Research article

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  32. The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, ...

    Authors: Min Zhang, Yi-Wei Tang, Ji Qi, Xin-Kai Liu, Dan-Feng Yan, Nai-Sheng Zhong, Nai-Qi Tao, Ji-Yin Gao, Yu-Guo Wang, Zhi-Ping Song, Ji Yang and Wen-Ju Zhang

    Citation: BMC Genomics 2019 20:828

    Content type: Research article

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  33. Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-path...

    Authors: Marco Tulio Solano-De la Cruz, Jacel Adame-García, Josefat Gregorio-Jorge, Verónica Jiménez-Jacinto, Leticia Vega-Alvarado, Lourdes Georgina Iglesias-Andreu, Esteban Elías Escobar-Hernández and Mauricio Luna-Rodríguez

    Citation: BMC Genomics 2019 20:826

    Content type: Research article

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  34. 5-Azacytidine (5-azaC) promotes the development of ‘Kyoho’ grape berry but the associated changes in gene expression have not been reported. In this study, we performed transcriptome analysis of grape berry at...

    Authors: Da-Long Guo, Qiong Li, Xiao-Ru Ji, Zhen-Guang Wang and Yi-He Yu

    Citation: BMC Genomics 2019 20:825

    Content type: Research article

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  35. Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internod...

    Authors: Lihang Qiu, Rongfa Chen, Yegeng Fan, Xing Huang, Hanmin Luo, Faqian Xiong, Junxian Liu, Ronghua Zhang, Jingchao Lei, Huiwen Zhou, Jianming Wu and Yangrui Li

    Citation: BMC Genomics 2019 20:817

    Content type: Research article

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  36. Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a pre...

    Authors: Shi-Fei Sang, De-Sheng Mei, Jia Liu, Qamar U. Zaman, Hai-Yan Zhang, Meng-Yu Hao, Li Fu, Hui Wang, Hong-Tao Cheng and Qiong Hu

    Citation: BMC Genomics 2019 20:813

    Content type: Research article

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  37. Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which lea...

    Authors: Renan Terassi Pinto, Natália Chagas Freitas, Wesley Pires Flausino Máximo, Thiago Bergamo Cardoso, Débora de Oliveira Prudente and Luciano Vilela Paiva

    Citation: BMC Genomics 2019 20:812

    Content type: Research article

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  38. Drought stress is a major limiting factor of soybean [Glycine max (L.) Merr.] production around the world. Soybean plants can ameliorate this stress with improved water-saving, sustained N2 fixation during water ...

    Authors: Clinton J. Steketee, Thomas R. Sinclair, Mandeep K. Riar, William T. Schapaugh and Zenglu Li

    Citation: BMC Genomics 2019 20:811

    Content type: Research article

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  39. Brassinosteroids (BRs) have a positive effect on many processes during plant growth and development, and in response to various abiotic stressors. Low-temperature (LT) stress constricts the geographic distribu...

    Authors: Mengru Zhao, Lingyun Yuan, Jie Wang, Shilei Xie, Yushan Zheng, Libing Nie, Shidong Zhu, Jinfeng Hou, Guohu Chen and Chenggang Wang

    Citation: BMC Genomics 2019 20:810

    Content type: Research article

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  40. Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genom...

    Authors: Hugo V. S. Rody, Renato G. H. Bombardelli, Silvana Creste, Luís E. A. Camargo, Marie-Anne Van Sluys and Claudia B. Monteiro-Vitorello

    Citation: BMC Genomics 2019 20:809

    Content type: Research article

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  41. Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this spe...

    Authors: Chunpu Qu, Hancheng Zhao, Jinyuan Chen, Zhuang Zuo, Xue Sun, Jiahuan Huang, Chengjun Yang, Xiuli Zhang, Peng Zhang, Xiankui Quan, Zhiru Xu and Guanjun Liu

    Citation: BMC Genomics 2019 20:801

    Content type: Research article

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  42. Reactive oxygen species (ROS) are generated by NADPH oxidases known as respiratory burst oxidase homologs (RBOHs) in plants. ROS regulate various cellular processes, including the mutualistic interactions betw...

    Authors: Citlali Fonseca-García, Alejandra E. Zayas, Jesús Montiel, Noreide Nava, Federico Sánchez and Carmen Quinto

    Citation: BMC Genomics 2019 20:800

    Content type: Research article

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  43. Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used ...

    Authors: Qing Lu, Yanbin Hong, Shaoxiong Li, Hao Liu, Haifen Li, Jianan Zhang, Haofa Lan, Haiyan Liu, Xingyu Li, Shijie Wen, Guiyuan Zhou, Rajeev K. Varshney, Huifang Jiang, Xiaoping Chen and Xuanqiang Liang

    Citation: BMC Genomics 2019 20:799

    Content type: Research article

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  44. Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling th...

    Authors: João Vitor Maldonado dos Santos, Everton Geraldo Capote Ferreira, André Luiz de Lima Passianotto, Bruna Bley Brumer, Adriana Brombini Dos Santos, Rafael Moreira Soares, Davoud Torkamaneh, Carlos Alberto Arrabal Arias, François Belzile, Ricardo Vilela Abdelnoor and Francismar Corrêa Marcelino-Guimarães

    Citation: BMC Genomics 2019 20:798

    Content type: Research article

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  45. Drought stress is one of the major factors that affects wheat yield. Glyceraldehyde-3-Phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays the important role in abiotic stress and plant devel...

    Authors: Lin Zhang, Zhiyong Xu, Haikun Ji, Ye Zhou and Shushen Yang

    Citation: BMC Genomics 2019 20:795

    Content type: Research article

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  46. Some Gynura species have been reported to be natural anti-diabetic plants. Improvement of their traits towards application relies on hybridization. Clearly, phylogenetic relationships could optimize compatible hy...

    Authors: Tianyu Han, Mimi Li, Jiawei Li, Han Lv, Bingru Ren, Jian Chen and Weilin Li

    Citation: BMC Genomics 2019 20:791

    Content type: Research article

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  47. Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation seq...

    Authors: Ke Teng, Wenjun Teng, Haifeng Wen, Yuesen Yue, Weier Guo, Juying Wu and Xifeng Fan

    Citation: BMC Genomics 2019 20:789

    Content type: Research article

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  48. The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive...

    Authors: Xiangpeng Leng, Hongru Wei, Xiaozhao Xu, Sandip A. Ghuge, Dongjie Jia, Gengsen Liu, Yongzhang Wang and Yongbing Yuan

    Citation: BMC Genomics 2019 20:786

    Content type: Research article

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  49. Artificial mutagenesis not only provides a new approach to increase the diversity of desirable traits for breeding new varieties but are also beneficial for characterizing the genetic basis of functional genes...

    Authors: Cong Tan, Xiao-Qi Zhang, Yin Wang, Dianxin Wu, Matthew I. Bellgard, Yanhao Xu, Xiaoli Shu, Gaofeng Zhou and Chengdao Li

    Citation: BMC Genomics 2019 20:783

    Content type: Research article

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