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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. Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves inv...

    Authors: Xuzixin Zhou, Yanbin Xue, Meiqin Mao, Yehua He, Mark Owusu Adjei, Wei Yang, Hao Hu, Jiawen Liu, Lijun Feng, Huiling Zhang, Jiaheng Luo, Xi Li, Lingxia Sun, Zhuo Huang and Jun Ma

    Citation: BMC Genomics 2021 22:331

    Content type: Research article

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  2. The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At...

    Authors: Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang and Jun Zhang

    Citation: BMC Genomics 2021 22:329

    Content type: Research article

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  3. HAK/KUP/KT (High-affinity K+ transporters/K+ uptake permeases/K+ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K+ uptake and transport, as well as biotic and abio...

    Authors: Kangfeng Cai, Fanrong Zeng, Junmei Wang and Guoping Zhang

    Citation: BMC Genomics 2021 22:317

    Content type: Research article

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  4. Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and...

    Authors: Hongjie Li, Jing Chen, Qi Zhao, Yilai Han, Li Li, Chunyu Sun, Kangyu Wang, Yanfang Wang, Mingzhu Zhao, Ping Chen, Jun Lei, Yi Wang and Meiping Zhang

    Citation: BMC Genomics 2021 22:316

    Content type: Research article

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  5. ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic co...

    Authors: Li Yan, Jianhong Zhang, Hongyu Chen and Hongmei Luo

    Citation: BMC Genomics 2021 22:315

    Content type: Research article

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  6. DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperat...

    Authors: Dan Li, Bian-E Feng, Yong-Jie Liu, Jie Gong, Yi-Miao Tang, Li-Ping Zhang, Bin-Shuang Pang, Ren-Wei Sun, Feng-Ting Zhang, Zhao-Bo Chen, Yong-Bo Wang, Xian-Chao Chen, Ai-Ping Wang, Chang-Ping Zhao and Shi-Qing Gao

    Citation: BMC Genomics 2021 22:310

    Content type: Research article

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  7. Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to under...

    Authors: Atsumi Ando, Ryan C. Kirkbride, Don C. Jones, Jane Grimwood and Z. Jeffrey Chen

    Citation: BMC Genomics 2021 22:309

    Content type: Research article

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  8. Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signa...

    Authors: Zhiwei Chen, Longhua Zhou, Panpan Jiang, Ruiju Lu, Nigel G. Halford and Chenghong Liu

    Citation: BMC Genomics 2021 22:300

    Content type: Research article

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  9. Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting...

    Authors: Liuyan Wang, Ruili Wang, Wei Lei, Jiayi Wu, Chenyang Li, Hongsong Shi, Lijiao Meng, Fang Yuan, Qingyuan Zhou and Cui Cui

    Citation: BMC Genomics 2021 22:299

    Content type: Research article

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  10. Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despit...

    Authors: Xiaoxiao Zou, Heroen Verbruggen, Tianjingwei Li, Jun Zhu, Zou Chen, Henqi He, Shixiang Bao and Jinhua Sun

    Citation: BMC Genomics 2021 22:298

    Content type: Research article

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  11. Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary ...

    Authors: Wenpan Dong, Yanlei Liu, Chao Xu, Yongwei Gao, Qingjun Yuan, Zhili Suo, Zhixiang Zhang and Jiahui Sun

    Citation: BMC Genomics 2021 22:293

    Content type: Research article

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  12. Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem...

    Authors: Sadhana Singh, Himabindu Kudapa, Vanika Garg and Rajeev K. Varshney

    Citation: BMC Genomics 2021 22:289

    Content type: Research article

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  13. Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton.

    Authors: Yuanhao Ding, Rui Zhang, Longfu Zhu, Maojun Wang, Yizan Ma, Daojun Yuan, Nian Liu, Haiyan Hu, Ling Min and Xianlong Zhang

    Citation: BMC Genomics 2021 22:277

    Content type: Research article

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  14. Fertilization in flowering plants depends on the early contact and acceptance of pollen grains by the receptive papilla cells of the stigma. Deciphering the specific transcriptomic response of both pollen and ...

    Authors: Chie Kodera, Jérémy Just, Martine Da Rocha, Antoine Larrieu, Lucie Riglet, Jonathan Legrand, Frédérique Rozier, Thierry Gaude and Isabelle Fobis-Loisy

    Citation: BMC Genomics 2021 22:268

    Content type: Research article

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  15. Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new techno...

    Authors: Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Hélène Muranty, Caroline Denancé, Luca Bianco, John Tillman and Eric van de Weg

    Citation: BMC Genomics 2021 22:246

    Content type: Research article

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  16. Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pe...

    Authors: Yun Dai, Xiao Sun, Chenggang Wang, Fei Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun and Shujiang Zhang

    Citation: BMC Genomics 2021 22:236

    Content type: Research article

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  17. Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased t...

    Authors: Jorge A. Ramírez-Tejero, Jaime Jiménez-Ruiz, Alicia Serrano, Angjelina Belaj, Lorenzo León, Raúl de la Rosa, Jesús Mercado-Blanco and Francisco Luque

    Citation: BMC Genomics 2021 22:229

    Content type: Research article

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  18. Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of ...

    Authors: Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse and Terence A. Brown

    Citation: BMC Genomics 2021 22:227

    Content type: Research article

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  19. B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryz...

    Authors: Xiuming Zhang, Li Zhang, Miaomiao Ji, Yifei Wu, Songlin Zhang, Yanxun Zhu, Jin Yao, Zhi Li, Hua Gao and Xiping Wang

    Citation: BMC Genomics 2021 22:221

    Content type: Research article

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  20. Persimmon (Diospyros kaki Thunb.) has various labile sex types, and studying its sex differentiation can improve breeding efficiency. However, studies on sexual regulation patterns in persimmon have focused mainl...

    Authors: Huawei Li, Liyuan Wang, Yini Mai, Weijuan Han, Yujing Suo, Songfeng Diao, Peng Sun and Jianmin Fu

    Citation: BMC Genomics 2021 22:203

    Content type: Research article

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  21. Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkalo...

    Authors: Alex Rajewski, Derreck Carter-House, Jason Stajich and Amy Litt

    Citation: BMC Genomics 2021 22:201

    Content type: Research article

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  22. Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important ec...

    Authors: Shoubo Tian, Panling Lu, Zhaohui Zhang, Jian Qiang Wu, Hui Zhang and Haibin Shen

    Citation: BMC Genomics 2021 22:194

    Content type: Research article

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  23. The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia),...

    Authors: Junjie Cui, Jiazhu Peng, Jiaowen Cheng and Kailin Hu

    Citation: BMC Genomics 2021 22:190

    Content type: Research article

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  24. Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cyc...

    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 2021 22:187

    Content type: Research article

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  25. Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of...

    Authors: Maricel Podio, Carolina Colono, Lorena Siena, Juan Pablo A. Ortiz and Silvina Claudia Pessino

    Citation: BMC Genomics 2021 22:185

    Content type: Research article

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  26. Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few la...

    Authors: Ying Wang, Hui-Liang Li, Yong-Kai Zhou, Dong Guo, Jia-Hong Zhu and Shi-Qing Peng

    Citation: BMC Genomics 2021 22:183

    Content type: Research article

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  27. Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season perennial forage grasses that is widely cultivated in the world and is highly tolerant to stressful conditions. However, little is kno...

    Authors: Zhongfu Yang, Gang Nie, Guangyan Feng, Jiating Han, Linkai Huang and Xinquan Zhang

    Citation: BMC Genomics 2021 22:178

    Content type: Research article

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  28. Finger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, b...

    Authors: Nathan D. Hall, Jinesh D. Patel, J. Scott McElroy and Leslie R. Goertzen

    Citation: BMC Genomics 2021 22:175

    Content type: Research article

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  29. Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake r...

    Authors: Mengjiao Yang, Cairong Wang, Muhammad Adeel Hassan, Faji Li, Xianchun Xia, Shubing Shi, Yonggui Xiao and Zhonghu He

    Citation: BMC Genomics 2021 22:174

    Content type: Research article

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  30. The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent econom...

    Authors: Dingding Cao, Zhongyuan Lin, Longyu Huang, Rebecca Njeri Damaris and Pingfang Yang

    Citation: BMC Genomics 2021 22:171

    Content type: Research article

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  31. Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific...

    Authors: Yan Cheng, Xiaoxue He, S. V. G. N. Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng, Ling Cao, Ping Zheng, Mohammad Aslam and Yuan Qin

    Citation: BMC Genomics 2021 22:167

    Content type: Research article

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  32. Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Ps...

    Authors: Thomas M. Adams, Tjelvar S. G. Olsson, Ricardo H. Ramírez-González, Ruth Bryant, Rosie Bryson, Pablo Eduardo Campos, Paul Fenwick, David Feuerhelm, Charlotte Hayes, Tina Henriksson, Amelia Hubbard, Radivoje Jevtić, Christopher Judge, Matthew Kerton, Jacob Lage, Clare M. Lewis…

    Citation: BMC Genomics 2021 22:166

    Content type: Database

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  33. Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration tr...

    Authors: Pawel Sega, Katarzyna Kruszka, Dawid Bielewicz, Wojciech Karlowski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska and Andrzej Pacak

    Citation: BMC Genomics 2021 22:165

    Content type: Research article

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  34. Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triter...

    Authors: Feng Wen, Xiaozhu Wu, Tongjian Li, Mingliang Jia, Xinsheng Liu and Liang Liao

    Citation: BMC Genomics 2021 22:161

    Content type: Research article

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  35. Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollinat...

    Authors: Ningthaipuilu Longmei, Gurjit Kaur Gill, Pervez Haider Zaidi, Ramesh Kumar, Sudha Krishnan Nair, Vermuri Hindu, Madhumal Thayil Vinayan and Yogesh Vikal

    Citation: BMC Genomics 2021 22:154

    Content type: Research article

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  36. Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its ...

    Authors: Tao-Xiong Shi, Rui-Yuan Li, Ran Zheng, Qing-Fu Chen, Hong-You Li, Juan Huang, Li-Wei Zhu and Cheng-Gang Liang

    Citation: BMC Genomics 2021 22:142

    Content type: Research article

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  37. Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant...

    Authors: Fuyun Hou, Taifeng Du, Zhen Qin, Tao Xu, Aixian Li, Shunxu Dong, Daifu Ma, Zongyun Li, Qingmei Wang and Liming Zhang

    Citation: BMC Genomics 2021 22:140

    Content type: Research article

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  38. Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grape...

    Authors: Xiangjing Yin, Yu Gao, Shiren Song, Danial Hassani and Jiang Lu

    Citation: BMC Genomics 2021 22:136

    Content type: Research article

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  39. The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative...

    Authors: Huatao Chen, Giriraj Kumawat, Yongliang Yan, Baojie Fan and Donghe Xu

    Citation: BMC Genomics 2021 22:132

    Content type: Research article

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  40. 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different develo...

    Authors: Shuo Wei, Wen Zhang, Rao Fu and Yang Zhang

    Citation: BMC Genomics 2021 22:126

    Content type: Research article

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  41. Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid bre...

    Authors: Xiaoli Geng, Yujie Qu, Yinhua Jia, Shoupu He, Zhaoe Pan, Liru Wang and Xiongming Du

    Citation: BMC Genomics 2021 22:123

    Content type: Research article

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  42. Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay ...

    Authors: Huan Wang, Zhaotang Ding, Mengjie Gou, Jianhui Hu, Yu Wang, Lu Wang, Yuchun Wang, Taimei Di, Xinfu Zhang, Xinyuan Hao, Xinchao Wang, Yajun Yang and Wenjun Qian

    Citation: BMC Genomics 2021 22:121

    Content type: Research article

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  43. Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses ...

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

    Citation: BMC Genomics 2021 22:113

    Content type: Research article

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  44. Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very li...

    Authors: Wei Wang, Lei Wang, Ling Wang, Meilian Tan, Collins O. Ogutu, Ziyan Yin, Jian Zhou, Jiaomei Wang, Lijun Wang and Xingchu Yan

    Citation: BMC Genomics 2021 22:109

    Content type: Research article

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