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Plant genomics

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

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  1. GGPP (geranylgeranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has...

    Authors: Faiza Ali, Ghulam Qanmber, Zhenzhen Wei, Daoqian Yu, Yong hui Li, Lei Gan, Fuguang Li and Zhi Wang

    Citation: BMC Genomics 2020 21:561

    Content type: Research article

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  2. High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that ...

    Authors: Chao He, Hong-Yu Zhang, Yong-Xin Zhang, Pei Fu, Li-Li You, Wen-Bo Xiao, Zhao-Hai Wang, Hai-Yan Song, Ying-Jin Huang and Jiang-Lin Liao

    Citation: BMC Genomics 2020 21:560

    Content type: Research article

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  3. Tea plant is one of the most important non-alcoholic beverage crops worldwide. While potassium (K+) is an essential macronutrient and greatly affects the growth and development of plants, the molecular mechanism ...

    Authors: Tianyuan Yang, Xin Lu, Yan Wang, Yunxia Xie, Jingzhen Ma, Xunmin Cheng, Enhua Xia, Xiaochun Wan and Zhaoliang Zhang

    Citation: BMC Genomics 2020 21:556

    Content type: Research article

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  4. The reblooming bearded iris (Iris germanica) can bloom twice a year, in spring and autumn. The extended ornamental period makes it more popular and brings additional commercial values. However, little is known ab...

    Authors: Zhuping Fan, Yike Gao, Yi Ren, Chunjing Guan, Rong Liu and Qixiang Zhang

    Citation: BMC Genomics 2020 21:553

    Content type: Research article

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  5. Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennial...

    Authors: Jing Liu, Fei Shen, Yao Xiao, Hongcheng Fang, Changpeng Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Xinzhong Zhang and Zhenhai Han

    Citation: BMC Genomics 2020 21:550

    Content type: Research article

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  6. Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choi...

    Authors: Jorge Villacrés-Vallejo, José Aranda-Ventura, Anna Wallis, Robin Cagle, Sara M. Handy, Jeffery Davis, Elizabeth Reed, Shu Zhang, Errol Strain, Monica Pava-Ripoll, David Erickson, Padmini Ramachandran and Andrea Ottesen

    Citation: BMC Genomics 2020 21:544

    Content type: Research article

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  7. Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative ...

    Authors: Sana Beji, Véronique Fontaine, Rosemonde Devaux, Martine Thomas, Sandra Silvia Negro, Nasser Bahrman, Mathieu Siol, Grégoire Aubert, Judith Burstin, Jean-Louis Hilbert, Bruno Delbreil and Isabelle Lejeune-Hénaut

    Citation: BMC Genomics 2020 21:536

    Content type: Research article

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  8. Water spinach (Ipomoea aquatica) is an important heat-resistant leafy vegetable that can survive under long-time heat stress condition. However, the physiological characteristics and molecular changes in its resp...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Xiaodong Chen and Gefu Wang-Pruski

    Citation: BMC Genomics 2020 21:533

    Content type: Research article

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  9. Alternanthera philoxeroides (alligator weed) is a highly invasive alien plant that has continuously and successfully expanded from the tropical to the temperate regions of China via asexual reproduction. During t...

    Authors: Landi Luo, Xiangxiang Kong, Zean Gao, Yan Zheng, Yunqiang Yang, Xiong Li, Danni Yang, Yupeng Geng and Yongping Yang

    Citation: BMC Genomics 2020 21:532

    Content type: Research article

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  10. Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve ...

    Authors: Chengwei Huang, Mao Yang, Danlei Shao, Yangming Wang, Shubei Wan, Jianbo He, Zuqing Meng and Rongzhan Guan

    Citation: BMC Genomics 2020 21:530

    Content type: Research article

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  11. Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature...

    Authors: Lin Fang, Xin Xu, Ji Li, Feng Zheng, Mingzhi Li, Jingwei Yan, Yuan Li, Xinhua Zhang, Lin Li, Guohua Ma, Aying Zhang, Fubing Lv, Kunlin Wu and Songjun Zeng

    Citation: BMC Genomics 2020 21:524

    Content type: Research article

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  12. Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for...

    Authors: Zena J. Rawandoozi, Timothy P. Hartmann, Silvia Carpenedo, Ksenija Gasic, Cassia da Silva Linge, Lichun Cai, Eric Van de Weg and David H. Byrne

    Citation: BMC Genomics 2020 21:522

    Content type: Research article

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  13. Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perenni...

    Authors: Zhi Wang, Wenjun Ma, Tianqing Zhu, Nan Lu, Fangqun Ouyang, Nan Wang, Guijuan Yang, Lisheng Kong, Guanzheng Qu, Shougong Zhang and Junhui Wang

    Citation: BMC Genomics 2020 21:508

    Content type: Research article

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  14. Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. sponta...

    Authors: Hongli Yang, Tianju Wang, Xinghua Yu, Yang Yang, Chunfang Wang, Qinghui Yang and Xianhong Wang

    Citation: BMC Genomics 2020 21:507

    Content type: Research article

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  15. Seasonal flowering time is an ecologically and economically important trait in temperate trees. Previous studies have shown that temperature in many tree species plays a pivotal role in regulating flowering ti...

    Authors: Jing-Jing Ma, Shuang-Wei Liu, Fang-Xu Han, Wei Li, Yue Li and Shi-Hui Niu

    Citation: BMC Genomics 2020 21:504

    Content type: Research article

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  16. The fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world. It is important to use resistant cultivars to manage the disease and minimize yield losses. ...

    Authors: Fuyou Fu, Xuehua Zhang, Fei Liu, Gary Peng, Fengqun Yu and Dilantha Fernando

    Citation: BMC Genomics 2020 21:501

    Content type: Research article

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  17. As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. Ho...

    Authors: Yang Zhang, Cong Liu, He Cheng, Shuanghui Tian, Yingying Liu, Shuang Wang, Huaxin Zhang, Muhammad Saqib, Hairong Wei and Zhigang Wei

    Citation: BMC Genomics 2020 21:498

    Content type: Research article

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  18. MicroRNAs (miRNAs) exhibit important regulatory roles in the response to abiotic stresses by post-transcriptionally regulating the target gene expression in plants. However, their functions in sesame response ...

    Authors: Yujuan Zhang, Huihui Gong, Donghua Li, Rong Zhou, Fengtao Zhao, Xiurong Zhang and Jun You

    Citation: BMC Genomics 2020 21:494

    Content type: Research article

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  19. Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo t...

    Authors: Amandeep Mittal, Inderjit Singh Yadav, Naresh Kumar Arora, Rajbir Singh Boora, Meenakshi Mittal, Parwinder Kaur, William Erskine, Parveen Chhuneja, Manav Indra Singh Gill and Kuldeep Singh

    Citation: BMC Genomics 2020 21:484

    Content type: Research article

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  20. Among several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Chinese jujube (Ziziphus jujuba Mill.) is a popular fruit tree species in Asia, and its fruits ...

    Authors: Yao Zhang, Weilin Gao, Hongtai Li, Yongkang Wang, Dengke Li, Chaoling Xue, Zhiguo Liu, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2020 21:483

    Content type: Research article

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  21. The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being exten...

    Authors: Jiangwei Qiao, Xiaojun Zhang, Biyun Chen, Fei Huang, Kun Xu, Qian Huang, Yi Huang, Qiong Hu and Xiaoming Wu

    Citation: BMC Genomics 2020 21:480

    Content type: Research article

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  22. Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-thro...

    Authors: Yadollah Shahryary, Rashmi R. Hazarika and Frank Johannes

    Citation: BMC Genomics 2020 21:479

    Content type: Software

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  23. Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial ...

    Authors: Xuejiao Liu, Panpan Meng, Guiyan Yang, Mengyan Zhang, Shaobing Peng and Mei Zhi Zhai

    Citation: BMC Genomics 2020 21:474

    Content type: Research article

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  24. VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress...

    Authors: Haley S. Toups, Noé Cochetel, Dennis Gray and Grant R. Cramer

    Citation: BMC Genomics 2020 21:472

    Content type: Research article

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  25. Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and ...

    Authors: Javaria Ashraf, Dongyun Zuo, Hailiang Cheng, Waqas Malik, Qiaolian Wang, Youping Zhang, Muhammad Ali Abid, Qiuhong Yang, Xiaoxu Feng, John Z. Yu and Guoli Song

    Citation: BMC Genomics 2020 21:470

    Content type: Research article

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  26. Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutr...

    Authors: Ghislain Kanfany, Desalegn D. Serba, Davina Rhodes, Paul St. Amand, Amy Bernardo, Prakash I Gangashetty, Ndjido Ardo Kane and Guihua Bai

    Citation: BMC Genomics 2020 21:469

    Content type: Research article

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  27. In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigat...

    Authors: A. Zombardo, C. Crosatti, P. Bagnaresi, L. Bassolino, N. Reshef, S. Puccioni, P. Faccioli, A. Tafuri, M. Delledonne, A. Fait, P. Storchi, L. Cattivelli and E. Mica

    Citation: BMC Genomics 2020 21:468

    Content type: Research article

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  28. Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of th...

    Authors: Kai Fan, Yunrui Chen, Zhijun Mao, Yao Fang, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang and Wenxiong Lin

    Citation: BMC Genomics 2020 21:465

    Content type: Research article

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  29. Tea plant (Camellia sinensis) is one of the world’s most important beverage crops due to its numerous secondary metabolites conferring tea quality and health effects. However, only a small fraction of tea genes (...

    Authors: Rui Zhang, Yong Ma, Xiaoyi Hu, Ying Chen, Xiaolong He, Ping Wang, Qi Chen, Chi-Tang Ho, Xiaochun Wan, Youhua Zhang and Shihua Zhang

    Citation: BMC Genomics 2020 21:461

    Content type: Database

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  30. Restoration of fertility (Rf) is an important trait for pigeonpea hybrid breeding. Few coarse quantitative trait locus (QTL) studies conducted in the past identified QTLs with large confidence intervals on the ge...

    Authors: Rachit K. Saxena, Johiruddin Molla, Pooja Yadav and Rajeev K. Varshney

    Citation: BMC Genomics 2020 21:460

    Content type: Research article

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  31. In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant develo...

    Authors: Daniel Restrepo-Montoya, Robert Brueggeman, Phillip E. McClean and Juan M. Osorno

    Citation: BMC Genomics 2020 21:459

    Content type: Research article

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  32. Multiple C2 domains and transmembrane region proteins (MCTPs) may act as transport mediators of other regulators. Although increased number of MCTPs in higher plants implies their diverse and specific functions i...

    Authors: Pengbo Hao, Hantao Wang, Liang Ma, Aimin Wu, Pengyun Chen, Shuaishuai Cheng, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:445

    Content type: Research article

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  33. The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress...

    Authors: Huilin Xiao, Chaoping Wang, Nadeem Khan, Mengxia Chen, Weihong Fu, Le Guan and Xiangpeng Leng

    Citation: BMC Genomics 2020 21:444

    Content type: Research article

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  34. Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophor...

    Authors: Benwen Liu, Yuxin Hu, Zhengyu Hu, Guoxiang Liu and Huan Zhu

    Citation: BMC Genomics 2020 21:442

    Content type: Research article

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  35. It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus.

    Authors: Xin Li, Xueru Liu, Xinyue Pang, Yong Yin, Huichun Yu, Yunxia Yuan and Bairu Li

    Citation: BMC Genomics 2020 21:437

    Content type: Research article

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  36. Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is ver...

    Authors: Amira M. I. Mourad, Vikas Belamkar and P. Stephen Baenziger

    Citation: BMC Genomics 2020 21:434

    Content type: Research article

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  37. The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated U...

    Authors: De Zhu, Ximei Li, Zhiwei Wang, Chunyuan You, Xinhui Nie, Jie Sun, Xianlong Zhang, Dawei Zhang and Zhongxu Lin

    Citation: BMC Genomics 2020 21:431

    Content type: Research article

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  38. Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to othe...

    Authors: Pratiti Dasgupta, Abhishek Das, Sambit Datta, Ishani Banerjee, Sucheta Tripathy and Shubho Chaudhuri

    Citation: BMC Genomics 2020 21:425

    Content type: Research article

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  39. Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-to...

    Authors: Fan Yan, Youcheng Zhu, Yanan Zhao, Ying Wang, Jingwen Li, Qingyu Wang and Yajing Liu

    Citation: BMC Genomics 2020 21:423

    Content type: Research article

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  40. Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In th...

    Authors: Kai Su, Huiyang Xing, Yinshan Guo, Fangyuan Zhao, Zhendong Liu, Kun Li, Yuanyuan Li and Xiuwu Guo

    Citation: BMC Genomics 2020 21:419

    Content type: Research article

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  41. Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters...

    Authors: Aurélien Chateigner, Marie-Claude Lesage-Descauses, Odile Rogier, Véronique Jorge, Jean-Charles Leplé, Véronique Brunaud, Christine Paysant-Le Roux, Ludivine Soubigou-Taconnat, Marie-Laure Martin-Magniette, Leopoldo Sanchez and Vincent Segura

    Citation: BMC Genomics 2020 21:416

    Content type: Research article

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  42. Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient di...

    Authors: Goon-Bo Kim, Chae Eun Lim, Jin-Seok Kim, Kyeonghee Kim, Jeong Hoon Lee, Hee-Ju Yu and Jeong-Hwan Mun

    Citation: BMC Genomics 2020 21:415

    Content type: Research article

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  43. Fulvic acid (FA) is a kind of plant growth regulator, which can promote plant growth, play an important role in fighting against drought, improve plant stress resistance, increase production and improve qualit...

    Authors: Jianhao Sun, Chen Qiu, Yiqian Ding, Yu Wang, Litao Sun, Kai Fan, Zhongshuai Gai, Guoqiang Dong, Jiguo Wang, Xinghui Li, Lubin Song and Zhaotang Ding

    Citation: BMC Genomics 2020 21:411

    Content type: Research article

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  44. Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially c...

    Authors: Zemao Yang, Zhigang Dai, Xiaojun Chen, Dongwei Xie, Qing Tang, Chaohua Cheng, Ying Xu, Canhui Deng, Chan Liu, Jiquan Chen and Jianguang Su

    Citation: BMC Genomics 2020 21:406

    Content type: Research article

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  45. Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development.

    Authors: Guohu Chen, Jian Wang, Hao Wang, Chenggang Wang, Xiaoyan Tang, Jie Li, Lei Zhang, Jianghua Song, Jinfeng Hou and Lingyun Yuan

    Citation: BMC Genomics 2020 21:401

    Content type: Research article

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  46. Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct i...

    Authors: Marie-Lara Bouffaud, Sylvie Herrmann, Mika T. Tarkka, Markus Bönn, Lasse Feldhahn and François Buscot

    Citation: BMC Genomics 2020 21:399

    Content type: Research article

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  47. The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has...

    Authors: Caitlin M. A. Simopoulos, Mitchell J. R. MacLeod, Solmaz Irani, Wilson W. L. Sung, Marc J. Champigny, Peter S. Summers, G. Brian Golding and Elizabeth A. Weretilnyk

    Citation: BMC Genomics 2020 21:396

    Content type: Research Article

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  48. Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the trans...

    Authors: Malachy T. Campbell, Qian Du, Kan Liu, Sandeep Sharma, Chi Zhang and Harkamal Walia

    Citation: BMC Genomics 2020 21:394

    Content type: Research Article

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