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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 36

  1. Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-to...

    Authors: Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:838

    Content type: Research article

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  2. Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in ...

    Authors: Bianca Büttner, Vera Draba, Klaus Pillen, Günther Schweizer and Andreas Maurer

    Citation: BMC Genomics 2020 21:837

    Content type: Research article

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  3. Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CC...

    Authors: Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:825

    Content type: Research article

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  4. The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’...

    Authors: Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan and Jun Wu

    Citation: BMC Genomics 2020 21:809

    Content type: Research article

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  5. Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilita...

    Authors: Chia-Chi Hsu, Shu-Yun Chen, Pei-Han Lai, Yu-Yun Hsiao, Wen-Chieh Tsai, Zhong-Jian Liu, Mei-Chu Chung, Olivier Panaud and Hong-Hwa Chen

    Citation: BMC Genomics 2020 21:807

    Content type: Research article

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  6. The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein transl...

    Authors: Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdul Latif Khan and Ahmed Al-Harrasi

    Citation: BMC Genomics 2020 21:804

    Content type: Research article

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  7. Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale me...

    Authors: Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin and Bowen Chen

    Citation: BMC Genomics 2020 21:803

    Content type: Research article

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  8. Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major p...

    Authors: Santiago Diaz, Daniel Ariza-Suarez, Paulo Izquierdo, Juan David Lobaton, Juan Fernando de la Hoz, Fernando Acevedo, Jorge Duitama, Alberto F. Guerrero, Cesar Cajiao, Victor Mayor, Stephen E. Beebe and Bodo Raatz

    Citation: BMC Genomics 2020 21:799

    Content type: Research article

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  9. Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots p...

    Authors: Ainhoa Calleja-Rodriguez, Jin Pan, Tomas Funda, Zhiqiang Chen, John Baison, Fikret Isik, Sara Abrahamsson and Harry X. Wu

    Citation: BMC Genomics 2020 21:796

    Content type: Research article

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  10. Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the VQ genes have been identified and their functions have be...

    Authors: Pengyun Chen, Fei wei, Shuaishuai Cheng, Liang Ma, Hantao Wang, Meng Zhang, Guangzhi Mao, Jianhua Lu, Pengbo Hao, Adeel Ahmad, Lijiao Gu, Qiang Ma, Aimin Wu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:795

    Content type: Research article

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  11. Stevia rebaudiana (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieti...

    Authors: Shaoshan Zhang, Qiong Liu, Chengcheng Lyu, Jinsong Chen, Renfeng Xiao, Jingtian Chen, Yunshu Yang, Huihui Zhang, Kai Hou and Wei Wu

    Citation: BMC Genomics 2020 21:794

    Content type: Research article

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  12. MYB superfamily is one of the most abundant families in plants, which plays important roles in plant growth, development, and productivity. However, to date, researches on MYBs in wheat (Triticum aestivum L.) are...

    Authors: Qiuhui Wei, Rong Chen, Xin Wei, Yuheng Liu, Shujuan Zhao, Xiaopu Yin and Tian Xie

    Citation: BMC Genomics 2020 21:792

    Content type: Research article

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  13. In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To rev...

    Authors: Da-Long Guo, Zhen-Guang Wang, Mao-Song Pei, Li-Li Guo and Yi-He Yu

    Citation: BMC Genomics 2020 21:784

    Content type: Research article

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  14. Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain ...

    Authors: Di Wu, Anqi Liu, Xiaoyu Qu, Jiayi Liang and Min Song

    Citation: BMC Genomics 2020 21:782

    Content type: Research article

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  15. The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptatio...

    Authors: Guodong Chen, Jizhong Wang, Xin Qiao, Cong Jin, Weike Duan, Xiaochuan Sun and Juyou Wu

    Citation: BMC Genomics 2020 21:781

    Content type: Research article

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  16. Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stre...

    Authors: Zahra Hajiahmadi, Amin Abedi, Hui Wei, Weibo Sun, Honghua Ruan, Qiang Zhuge and Ali Movahedi

    Citation: BMC Genomics 2020 21:778

    Content type: Research article

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  17. Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distingu...

    Authors: Oumar Diack, Ghislain Kanfany, Mame Codou Gueye, Ousmane Sy, Amadou Fofana, Hamidou Tall, Desalegn D. Serba, Leila Zekraoui, Cécile Berthouly-Salazar, Yves Vigouroux, Diaga Diouf and Ndjido Ardo Kane

    Citation: BMC Genomics 2020 21:777

    Content type: Research article

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  18. Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, know...

    Authors: Hui Xia, Xiaosong Ma, Kai Xu, Lei Wang, Hongyan Liu, Liang Chen and Lijun Luo

    Citation: BMC Genomics 2020 21:776

    Content type: Research article

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  19. Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental pro...

    Authors: Wenrui Li, Chuangfeng Liu, Jingling Liu, Zhenqing Bai and Zongsuo Liang

    Citation: BMC Genomics 2020 21:727

    Content type: Research article

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  20. Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits,...

    Authors: Liang Wang, Brima Conteh, Linzhi Fang, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:739

    Content type: Research article

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  21. Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory ...

    Authors: Mohammad Aslam, Bello Hassan Jakada, Beenish Fakher, Joseph G. Greaves, Xiaoping Niu, Zhenxia Su, Yan Cheng, Shijiang Cao, Xiaomei Wang and Yuan Qin

    Citation: BMC Genomics 2020 21:735

    Content type: Research article

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  22. Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transc...

    Authors: Zhaoxi Zhou, Hongmao Gao, Jianhong Ming, Zheli Ding, Xing’e Lin and Rulin Zhan

    Citation: BMC Genomics 2020 21:734

    Content type: Research article

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  23. The ray floret shapes referred to as petal types on the chrysanthemum (Chrysanthemum × morifolium Ramat.) capitulum is extremely abundant, which is one of the most important ornamental traits of chrysanthemum. Ho...

    Authors: Ya Pu, He Huang, Xiaohui Wen, Chenfei Lu, Bohan Zhang, Xueqi Gu, Shuai Qi, Guangxun Fan, Wenkui Wang and Silan Dai

    Citation: BMC Genomics 2020 21:728

    Content type: Research article

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  24. Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and ...

    Authors: Wenkai Du, Lihua Ning, Yongshun Liu, Shixi Zhang, Yuming Yang, Qing Wang, Shengqian Chao, Hui Yang, Fang Huang, Hao Cheng and Deyue Yu

    Citation: BMC Genomics 2020 21:725

    Content type: Research article

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  25. The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The A...

    Authors: Nadeem Khan, Frank M. You, Raju Datla, Sridhar Ravichandran, Bosen Jia and Sylvie Cloutier

    Citation: BMC Genomics 2020 21:722

    Content type: Research article

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  26. We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 mod...

    Authors: Biruk A. Feyissa, Justin Renaud, Vida Nasrollahi, Susanne E. Kohalmi and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:721

    Content type: Research article

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  27. To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a sma...

    Authors: Gracia Zabala, Anupreet Kour and Lila O. Vodkin

    Citation: BMC Genomics 2020 21:716

    Content type: Research article

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  28. As global warming continues, heat stress (HS) is becoming an increasingly significant factor limiting plant growth and reproduction, especially for cool-season grass species. The objective of this study was to...

    Authors: Qi Yan, Xifang Zong, Fan Wu, Jie Li, Tiantian Ma, Yufeng Zhao, Qian Ma, Penglei Wang, Yanrong Wang and Jiyu Zhang

    Citation: BMC Genomics 2020 21:715

    Content type: Research article

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  29. The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CL...

    Authors: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi and Bo Zheng

    Citation: BMC Genomics 2020 21:709

    Content type: Methodology article

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  30. Lotus is an aquatic horticultural crop that is widely cultivated in most regions of China and is used as an important off-season vegetable. The principal root of lotus is degenerated, and adventitious roots (A...

    Authors: Cheng Libao, Han Yuyan, Zhao Minrong, Xu Xiaoyong, Shen Zhiguang, Wang Chunfei, Li Shuyan and Hu Zhubing

    Citation: BMC Genomics 2020 21:707

    Content type: Research article

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  31. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes mo...

    Authors: Tao Hu, Tao Wang, Huiying Li, Misganaw Wassie, Huawei Xu and Liang Chen

    Citation: BMC Genomics 2020 21:696

    Content type: Research article

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  32. MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different p...

    Authors: Shu-Yun Chen, Mei-Hsiu Su, Karl A. Kremling, Nicholas K. Lepak, M. Cinta Romay, Qi Sun, Peter J. Bradbury, Edward S. Buckler and Hsin-Mei Ku

    Citation: BMC Genomics 2020 21:689

    Content type: Research article

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  33. APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2...

    Authors: Peiting Li, Zhe Chai, Pingping Lin, Chaohua Huang, Guoqiang Huang, Liangnian Xu, Zuhu Deng, Muqing Zhang, Yu Zhang and Xinwang Zhao

    Citation: BMC Genomics 2020 21:685

    Content type: Research article

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  34. Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family o...

    Authors: Shashank Kumar Yadav, Vinjamuri Venkata Santosh Kumar, Rakesh Kumar Verma, Pragya Yadav, Ankit Saroha, Dhammaprakash Pandhari Wankhede, Bhupendra Chaudhary and Viswanathan Chinnusamy

    Citation: BMC Genomics 2020 21:676

    Content type: Research article

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  35. The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucr...

    Authors: Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernanda Zatti Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert James Henry, Monalisa Sampaio Carneiro and Gabriel Rodrigues Alves Margarido

    Citation: BMC Genomics 2020 21:673

    Content type: Research article

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  36. The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of ...

    Authors: S. Dhivya, S. Ashutosh, I. Gowtham, V. Baskar, A. Baala Harini, S. Mukunthakumar and R. Sathishkumar

    Citation: BMC Genomics 2020 21:659

    Content type: Research article

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  37. Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant speci...

    Authors: Yuliya A. Putintseva, Eugeniya I. Bondar, Evgeniy P. Simonov, Vadim V. Sharov, Natalya V. Oreshkova, Dmitry A. Kuzmin, Yuri M. Konstantinov, Vladimir N. Shmakov, Vadim I. Belkov, Michael G. Sadovsky, Olivier Keech and Konstantin V. Krutovsky

    Citation: BMC Genomics 2020 21:654

    Content type: Research article

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  38. In China, lotus is an important cultivated crop with multiple applications in ornaments, food, and environmental purification. Adventitious roots (ARs), a secondary root is necessary for the uptake of nutritio...

    Authors: Cheng libao, Zhao minrong, Hu Zhubing, Liu huiying and Li Shuyan

    Citation: BMC Genomics 2020 21:653

    Content type: Research article

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  39. The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene...

    Authors: Bobo Song, Zikai Tang, Xiaolong Li, Jiaming Li, Mingyue Zhang, Kejiao Zhao, Hainan Liu, Shaoling Zhang and Jun Wu

    Citation: BMC Genomics 2020 21:644

    Content type: Research article

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  40. Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is...

    Authors: Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Xu Yang, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang and Shuxun Yu

    Citation: BMC Genomics 2020 21:643

    Content type: Research article

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  41. Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness an...

    Authors: Weifang Liao, Zhinan Mei, Lihong Miao, Pulin Liu and Ruijie Gao

    Citation: BMC Genomics 2020 21:639

    Content type: Research article

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  42. Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca

    Authors: Hui Liu, Wei Qu, Kaikai Zhu and Zong-Ming ( Max) Cheng

    Citation: BMC Genomics 2020 21:635

    Content type: Research article

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  43. The contribution of mitogen-activated protein kinase (MAPK) cascades to plant growth and development has been widely studied, but this knowledge has not yet been extended to the medicinal plant Salvia miltiorrhiz...

    Authors: Yongfeng Xie, Meiling Ding, Bin Zhang, Jie Yang, Tianlin Pei, Pengda Ma and Juane Dong

    Citation: BMC Genomics 2020 21:630

    Content type: Research article

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  44. Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms ar...

    Authors: Ben N. Mansfeld, Marivi Colle, Chunqiu Zhang, Ying-Chen Lin and Rebecca Grumet

    Citation: BMC Genomics 2020 21:628

    Content type: Research article

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  45. Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in...

    Authors: Archita Chatterjee, Abhirup Paul, G. Meher Unnati, Ruchika Rajput, Trisha Biswas, Tamalika Kar, Srijita Basak, Neelam Mishra, Ashutosh Pandey and Anurag Prakash Srivastava

    Citation: BMC Genomics 2020 21:613

    Content type: Research article

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  46. Anthocyanins determinate the flower color of many plants. Tobacco is a model plant for studying the molecular regulation of flower coloration. We investigated the mechanism underlying flower coloration in toba...

    Authors: Fangchan Jiao, Lu Zhao, Xingfu Wu, Zhongbang Song and Yongping Li

    Citation: BMC Genomics 2020 21:611

    Content type: Research article

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  47. Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely sup...

    Authors: Yao Xiao, Fei Yi, Juanjuan Ling, Guijuan Yang, Na Lu, Zirui Jia, Junchen Wang, Kun Zhao, Junhui Wang and Wenjun Ma

    Citation: BMC Genomics 2020 21:609

    Content type: Research article

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