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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 28

  1. Content type: Research article

    Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean (Glycine max L. Merr) that have important roles in providing defense against pathogens. They also have impre...

    Authors: Md Asraful Jahan, Brianna Harris, Matthew Lowery, Katie Coburn, Aniello M. Infante, Ryan J. Percifield, Amanda G. Ammer and Nik Kovinich

    Citation: BMC Genomics 2019 20:149

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  2. Content type: Research article

    Trichoderma spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of Trichoderma-induced plant resistance is not fully understood. In this study, a novel Trichoderma strain was identif...

    Authors: Min Yuan, Yuanyuan Huang, Weina Ge, Zhenhua Jia, Shuishan Song, Lan Zhang and Yali Huang

    Citation: BMC Genomics 2019 20:144

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  3. Content type: Research article

    Carbonic anhydrase (CA) catalyzes the hydration of CO2 in the first biochemical step of C4 photosynthesis, and has been considered a potentially rate-limiting step when CO2 availability within a leaf is low. Prev...

    Authors: Allison R. Kolbe, Anthony J. Studer, Omar E. Cornejo and Asaph B. Cousins

    Citation: BMC Genomics 2019 20:138

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  4. Content type: Research article

    Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to...

    Authors: Xinyou Cao, Liqin Hu, Xueyan Chen, Rongzhi Zhang, Dungong Cheng, Haosheng Li, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Aifeng Liu, Jianming Song, Cheng Liu, Jianjun Liu, Zhendong Zhao, Ming Chen and Youzhi Ma

    Citation: BMC Genomics 2019 20:136

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  5. Content type: Research article

    Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

    Authors: Kathleen DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Ling-Ling Gao, Karen Frick and Karam B. Singh

    Citation: BMC Genomics 2019 20:135

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  6. Content type: Software

    MicroRNAs (miRNAs) constitute a well-known small RNA (sRNA) species with important regulatory roles. To date, several bioinformatics tools have been developed for large-scale prediction of miRNAs based on high...

    Authors: Dongliang Yu, Ying Wan, Hidetaka Ito, Xiaoxia Ma, Tian Xie, Tingzhang Wang, Chaogang Shao and Yijun Meng

    Citation: BMC Genomics 2019 20:133

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  7. Content type: Research article

    Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolution...

    Authors: Desre Pinard, Alexander A. Myburg and Eshchar Mizrachi

    Citation: BMC Genomics 2019 20:132

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  8. Content type: Research article

    Warm winter and hot spring attributed to global warming affected floral development and may induce floral abortion, resulted in poor flowering in litchi. To identify genes potentially involved in litchi floral...

    Authors: Hao Liu, Congcong Wang, Houbin Chen and Biyan Zhou

    Citation: BMC Genomics 2019 20:127

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  9. Content type: Research article

    Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to t...

    Authors: Qi Xu, Songtai Wang, Huazhu Hong and Yin Zhou

    Citation: BMC Genomics 2019 20:125

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  10. Content type: Research article

    Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect ...

    Authors: Sheng-Hui Jiang, Qing-Guo Sun, Min Chen, Nan Wang, Hai-Feng Xu, Hong-Cheng Fang, Yi-Cheng Wang, Zong-Ying Zhang and Xue-Sen Chen

    Citation: BMC Genomics 2019 20:117

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  11. Content type: Research article

    The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, the...

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

    Citation: BMC Genomics 2019 20:113

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  12. Content type: Research article

    Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic...

    Authors: Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Johnie N. Jenkins, Jack C. McCarty and Christopher B. Florane

    Citation: BMC Genomics 2019 20:112

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  13. Content type: Research article

    Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available fo...

    Authors: Luana P. Gonçalves, Raquel L. Boscariol Camargo, Marco Aurélio Takita, Marcos A. Machado, Walter S. dos Soares Filho and Marcio G. C. Costa

    Citation: BMC Genomics 2019 20:110

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  14. Content type: Research article

    Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The fl...

    Authors: Cristian Vergara-Pulgar, Karin Rothkegel, Mauricio González-Agüero, Romina Pedreschi, Reinaldo Campos-Vargas, Bruno G. Defilippi and Claudio Meneses

    Citation: BMC Genomics 2019 20:108

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  15. Content type: Research article

    Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXL...

    Authors: Zhisheng Han, Yanlin Liu, Xiong Deng, Dongmiao Liu, Yue Liu, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2019 20:101

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  16. Content type: Research article

    RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – ...

    Authors: Per K. I. Wilhelmsson, Jake O. Chandler, Noe Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner-Metzger and Stefan A. Rensing

    Citation: BMC Genomics 2019 20:95

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  17. Content type: Research article

    As important female reproductive tissues, the rice (Oryza sativa L.) ovule and female gametophyte is significant in terms of their fertility. Long noncoding RNAs (lncRNAs) play important and wide-ranging roles in...

    Authors: Helian Liu, Ruihua Wang, Bigang Mao, Bingran Zhao and Jianbo Wang

    Citation: BMC Genomics 2019 20:90

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  18. Content type: Research article

    Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flo...

    Authors: Chakkree Lekklar, Monnat Pongpanich, Duangjai Suriya-arunroj, Aumnart Chinpongpanich, Helen Tsai, Luca Comai, Supachitra Chadchawan and Teerapong Buaboocha

    Citation: BMC Genomics 2019 20:76

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  20. Content type: Research article

    The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genom...

    Authors: Xue Zhao, Haipeng Jiang, Lei Feng, Yingfan Qu, Weili Teng, Lijuan Qiu, Hongkun Zheng, Yingpeng Han and Wenbin Li

    Citation: BMC Genomics 2019 20:68

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  22. Content type: Research article

    Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. ...

    Authors: Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad and Youxiong Que

    Citation: BMC Genomics 2019 20:57

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  23. Content type: Research article

    Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January–March and a period of low temperature is neces...

    Authors: Fengxi Yang, Genfa Zhu, Yonglu Wei, Jie Gao, Gang Liang, Lingyuan Peng, Chuqiao Lu and Jianpeng Jin

    Citation: BMC Genomics 2019 20:53

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  24. Content type: Research article

    Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in pea...

    Authors: Zhihui Wang, Liying Yan, Liyun Wan, Dongxin Huai, Yanping Kang, Lei Shi, Huifang Jiang, Yong Lei and Boshou Liao

    Citation: BMC Genomics 2019 20:51

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  25. Content type: Research article

    Red-fleshed papaya is a good material to study the different carotenoids accumulation mechanism in the peel and flesh. Although the peel and flesh of papaya closely integrated into one body, the flesh colorati...

    Authors: Yan Hong Shen, Fei Ying Yang, Bing Guo Lu, Wan Wan Zhao, Tao Jiang, Li Feng, Xiao Jing Chen and Ray Ming

    Citation: BMC Genomics 2019 20:49

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  26. Content type: Research article

    Taste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain uncle...

    Authors: Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng and Wanpeng Xi

    Citation: BMC Genomics 2019 20:45

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  27. Content type: Research article

    Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways...

    Authors: Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone and Maria Manuela Rigano

    Citation: BMC Genomics 2019 20:43

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  28. Content type: Research article

    The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode...

    Authors: Margaret Worthington, Masumi Ebina, Naoki Yamanaka, Christopher Heffelfinger, Constanza Quintero, Yeny Patricia Zapata, Juan Guillermo Perez, Michael Selvaraj, Manabu Ishitani, Jorge Duitama, Juan Fernando de la Hoz, Idupulapati Rao, Stephen Dellaporta, Joe Tohme and Jacobo Arango

    Citation: BMC Genomics 2019 20:41

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  29. Content type: Research article

    Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that pla...

    Authors: Hong Zhu, Yu Zhang, Ruifang Tang, Hongxia Qu, Xuewu Duan and Yueming Jiang

    Citation: BMC Genomics 2019 20:33

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  30. Content type: Research article

    Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants la...

    Authors: Rongzhi Zhang, Shuaifeng Geng, Zhengrui Qin, Zongxiang Tang, Cheng Liu, Dongfeng Liu, Guoqi Song, Yulian Li, Shujuan Zhang, Wei Li, Jie Gao, Xiaodong Han and Genying Li

    Citation: BMC Genomics 2019 20:29

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  31. Content type: Research article

    B-box (BBX) proteins play important roles in plant growth regulation and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses.

    Authors: Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiao-Yong Wei, Qiong-Qiong Chen, Wen-Qiang Li, Wen-Ting Liu and Kun-Ming Chen

    Citation: BMC Genomics 2019 20:27

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  32. Content type: Research article

    Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus an...

    Authors: Chia-Chi Hsu, Pei-Han Lai, Tien-Chih Chen, Wen-Chieh Tsai, Jui-Lin Hsu, Yu-Yun Hsiao, Wen-Luan Wu, Ching-Hsiu Tsai, Wen-Huei Chen and Hong-Hwa Chen

    Citation: BMC Genomics 2019 20:25

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  33. Content type: Research article

    Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candid...

    Authors: Wenxian Liang, Lin Ni, Rebeca Carballar-Lejarazú, Xiaoxing Zou, Weihong Sun, Lingjiao Wu, Xueyuan Yuan, Yanling Mao, Wei Huang and Shuangquan Zou

    Citation: BMC Genomics 2019 20:24

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  34. Content type: Research article

    Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QT...

    Authors: Hongju Jian, Aoxiang Zhang, Jinqi Ma, Tengyue Wang, Bo Yang, Lan Shuan Shuang, Min Liu, Jiana Li, Xinfu Xu, Andrew H. Paterson and Liezhao Liu

    Citation: BMC Genomics 2019 20:21

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  35. Content type: Research article

    Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is imp...

    Authors: Hyeon Seok Lee, Woon Ha Hwang, Jae Hyeok Jeong, Seung Hyeon Ahn, Jeong Seon Baek, Han Yong Jeong, Hong Kyu Park, Bon Il Ku, Jong Tak Yun, Geon Hwi Lee and Kyung Jin Choi

    Citation: BMC Genomics 2019 20:18

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  36. Content type: Research article

    It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.

    Authors: Yanling Ma, Miao Liu, Jiri Stiller and Chunji Liu

    Citation: BMC Genomics 2019 20:12

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  37. Content type: Research article

    Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylo...

    Authors: Min Xu, Cheng-Li Liu, Juan Luo, Zhao Qi, Zhen Yan, Yu Fu, Shuang-Shuang Wei and Hua Tang

    Citation: BMC Genomics 2019 20:10

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  38. Content type: Research article

    Celastrus angulatus Maxim is a kind of crucial and traditional insecticidal plant widely distributed in the mountains of southwest China. Celangulin V is the efficient insecticidal sesquiterpenoid of C. angulatus

    Authors: Weiguo Li, Ranran Xu, Xiaoguang Yan, Dongmei Liang, Lei Zhang, Xiaoyu Qin, Qinggele Caiyin, Guangrong Zhao, Wenhai Xiao, Zhaonong Hu and Jianjun Qiao

    Citation: BMC Genomics 2019 20:7

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  40. Content type: Research article

    Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the differe...

    Authors: Yingdan Yuan, Maoyun Yu, Zhaohui Jia, Xue’er Song, Yingquan Liang and Jinchi Zhang

    Citation: BMC Genomics 2018 19:978

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  41. Content type: Methodology article

    Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology. Correctly asse...

    Authors: Weiwen Wang, Miriam Schalamun, Alejandro Morales-Suarez, David Kainer, Benjamin Schwessinger and Robert Lanfear

    Citation: BMC Genomics 2018 19:977

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  43. Content type: Research article

    Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are...

    Authors: Liwei Zheng, Juanjuan Ma, Jiangping Mao, Sheng Fan, Dong Zhang, Caiping Zhao, Na An and Mingyu Han

    Citation: BMC Genomics 2018 19:962

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  44. Content type: Research article

    Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content ...

    Authors: Li-Yi Xu, Li-Yuan Wang, Kang Wei, Li-Qiang Tan, Jing-Jing Su and Hao Cheng

    Citation: BMC Genomics 2018 19:955

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  45. Content type: Research article

    Guar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted ...

    Authors: Omika Thakur and Gursharn Singh Randhawa

    Citation: BMC Genomics 2018 19:951

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  46. Content type: Research article

    Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primar...

    Authors: Sui Wang, Chuanping Yang, Xiyang Zhao, Su Chen and Guan-Zheng Qu

    Citation: BMC Genomics 2018 19:950

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  47. Content type: Research article

    Genomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Pice...

    Authors: Zhi-Qiang Chen, John Baison, Jin Pan, Bo Karlsson, Bengt Andersson, Johan Westin, María Rosario García-Gil and Harry X. Wu

    Citation: BMC Genomics 2018 19:946

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  48. Content type: Research article

    Root-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cell...

    Authors: Clémence Medina, Martine da Rocha, Marc Magliano, Alizée Raptopoulo, Nathalie Marteu, Kevin Lebrigand, Pierre Abad, Bruno Favery and Stéphanie Jaubert-Possamai

    Citation: BMC Genomics 2018 19:943

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  49. Content type: Research article

    Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that shoul...

    Authors: Aïda Azaiez, Nathalie Pavy, Sébastien Gérardi, Jérôme Laroche, Brian Boyle, France Gagnon, Marie-Josée Mottet, Jean Beaulieu and Jean Bousquet

    Citation: BMC Genomics 2018 19:942

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  50. Content type: Research article

    Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for t...

    Authors: Amanda Huen, Julia Bally and Penelope Smith

    Citation: BMC Genomics 2018 19:940

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