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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 33

  1. The non-climacteric ‘Yellow’ melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related p...

    Authors: Michelle Orane Schemberger, Marília Aparecida Stroka, Letícia Reis, Kamila Karoline de Souza Los, Gillize Aparecida Telles de Araujo, Michelle Zibetti Tadra Sfeir, Carolina Weigert Galvão, Rafael Mazer Etto, Amanda Regina Godoy Baptistão and Ricardo Antonio Ayub

    Citation: BMC Genomics 2020 21:262

    Content type: Research article

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  2. The Mi-1 gene was the first identified and cloned gene that provides resistance to root-knot nematodes (RKNs) in cultivated tomato. However, owing to its temperature sensitivity, this gene does not meet the need ...

    Authors: Chong Du, Jingbin Jiang, He Zhang, Tingting Zhao, Huanhuan Yang, Dongye Zhang, Zhentong Zhao, Xiangyang Xu and Jingfu Li

    Citation: BMC Genomics 2020 21:250

    Content type: Research article

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  3. Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular bree...

    Authors: Wei Shi, Shao-Lu Zhao, Kai Liu, Yi-Biao Sun, Zheng-Bin Ni, Gui-Yun Zhang, Hong-Sheng Tang, Jing-Wen Zhu, Bai-Jie Wan, Hong-Qin Sun, Jin-Ying Dai, Ming-Fa Sun, Guo-Hong Yan, Ai-Min Wang and Guo-Yong Zhu

    Citation: BMC Genomics 2020 21:245

    Content type: Research article

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  4. Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate...

    Authors: Rongrong Zhai, Shenghai Ye, Guofu Zhu, Yanting Lu, Jing Ye, Faming Yu, Qiren Chu and Xiaoming Zhang

    Citation: BMC Genomics 2020 21:238

    Content type: Research article

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  5. Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposo...

    Authors: Rafael de Assis, Viviane Yumi Baba, Leonardo Adabo Cintra, Leandro Simões Azeredo Gonçalves, Rosana Rodrigues and André Luís Laforga Vanzela

    Citation: BMC Genomics 2020 21:237

    Content type: Research article

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  6. Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the...

    Authors: Xiao-Yong Zhang, Jie-Ya Qiu, Qiu-Ling Hui, Yuan-Yuan Xu, Yi-Zhong He, Liang-Zhi Peng and Xing-Zheng Fu

    Citation: BMC Genomics 2020 21:233

    Content type: Research article

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  7. Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, dev...

    Authors: Hui Xia, Shunwu Yu, Deyan Kong, Jie Xiong, Xiaosong Ma, Liang Chen and Lijun Luo

    Citation: BMC Genomics 2020 21:232

    Content type: Research article

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  8. Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF...

    Authors: Jeky Chanwala, Suresh Satpati, Anshuman Dixit, Ajay Parida, Mrunmay Kumar Giri and Nrisingha Dey

    Citation: BMC Genomics 2020 21:231

    Content type: Research article

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  9. The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefo...

    Authors: Xuke Lu, Na Shu, Delong Wang, Junjuan Wang, Xiugui Chen, Binglei Zhang, Shuai Wang, Lixue Guo, Chao Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:213

    Content type: Research article

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  10. Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been cha...

    Authors: Lili Fu, Zehong Ding, Deguan Tan, Bingying Han, Xuepiao Sun and Jiaming Zhang

    Citation: BMC Genomics 2020 21:212

    Content type: Research article

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  11. Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular...

    Authors: Fengdan Guo, Junjie Ma, Lei Hou, Suhua Shi, Jinbo Sun, Guanghui Li, Chuanzhi Zhao, Han Xia, Shuzhen Zhao, Xingjun Wang and Yanxiu Zhao

    Citation: BMC Genomics 2020 21:211

    Content type: Research article

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  12. Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will fac...

    Authors: Guohao Han, Shiyu Liu, Yuli Jin, Mengshu Jia, Pengtao Ma, Hong Liu, Jing Wang and Diaoguo An

    Citation: BMC Genomics 2020 21:206

    Content type: Research article

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  13. Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS...

    Authors: Anthony Bernard, Annarita Marrano, Armel Donkpegan, Patrick J. Brown, Charles A. Leslie, David B. Neale, Fabrice Lheureux and Elisabeth Dirlewanger

    Citation: BMC Genomics 2020 21:203

    Content type: Research article

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  14. Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at ...

    Authors: Katie O’Connor, Ben Hayes, Craig Hardner, Catherine Nock, Abdul Baten, Mobashwer Alam, Robert Henry and Bruce Topp

    Citation: BMC Genomics 2020 21:199

    Content type: Research article

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  15. Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt str...

    Authors: Mohamed Hamed Arisha, Hesham Aboelnasr, Muhammad Qadir Ahmad, Yaju Liu, Wei Tang, Runfei Gao, Hui Yan, Meng Kou, Xin Wang, Yungang Zhang and Qiang Li

    Citation: BMC Genomics 2020 21:197

    Content type: Research article

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  16. Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic div...

    Authors: Nancy Manchanda, John L. Portwood II, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf and Matthew B. Hufford

    Citation: BMC Genomics 2020 21:193

    Content type: Software

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  17. Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. H...

    Authors: Lixin Wang, Min Li, Zhiguo Liu, Li Dai, Mengling Zhang, Lili Wang, Jin Zhao and Mengjun Liu

    Citation: BMC Genomics 2020 21:191

    Content type: Research article

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  19. MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industr...

    Authors: Zhengmei Yang, Panpan Zhu, Hunseung Kang, Lin Liu, Qinghe Cao, Jian Sun, Tingting Dong, Mingku Zhu, Zongyun Li and Tao Xu

    Citation: BMC Genomics 2020 21:164

    Content type: Research article

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  20. Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3)....

    Authors: Nourolah Soltani, Teo Best, Dantria Grace, Christen Nelms, Ketia Shumaker, Jeanne Romero-Severson, Daniela Moses, Stephan Schuster, Margaret Staton, John Carlson and Kimberly Gwinn

    Citation: BMC Genomics 2020 21:160

    Content type: Research article

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  21. Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analys...

    Authors: Heli Chen, Zhiyu Hao, Yunfeng Zhao and Runqing Yang

    Citation: BMC Genomics 2020 21:151

    Content type: Research article

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  22. Lotus (Nelumbo nucifera) is an aquatic plant with important agronomic, horticulture, art and religion values. It was the basal eudicot species occupying a critical phylogenetic position in flowering plants. After...

    Authors: Ye Li, Feng-Lin Zhu, Xing-Wen Zheng, Man-Li Hu, Chen Dong, Ying Diao, You-Wei Wang, Ke-Qiang Xie and Zhong-Li Hu

    Citation: BMC Genomics 2020 21:146

    Content type: Research article

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  23. The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxal...

    Authors: Bidisha Bhowal, Sneh L. Singla-Pareek, Sudhir K. Sopory and Charanpreet Kaur

    Citation: BMC Genomics 2020 21:145

    Content type: Research article

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  24. The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6, was cloned and applied in rice breeding to effecti...

    Authors: Jiaoyan Tan, Yan Wu, Jianping Guo, Huimin Li, Lili Zhu, Rongzhi Chen, Guangcun He and Bo Du

    Citation: BMC Genomics 2020 21:144

    Content type: Research article

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  25. Mitogen-activated protein kinase (MAPK) cascades play vital roles in signal transduction in response to a wide range of biotic and abiotic stresses. In a previous study, we identified ten ZjMAPKs and five ZjMAPKK...

    Authors: Zhiguo Liu, Lixin Wang, Chaoling Xue, Yuetong Chu, Weilin Gao, Yitong Zhao, Jin Zhao and Mengjun Liu

    Citation: BMC Genomics 2020 21:142

    Content type: Research article

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  26. Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C4 photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal gras...

    Authors: Tianpeng Liu, Jihong He, Kongjun Dong, Xuewen Wang, Wenwen Wang, Peng Yang, Ruiyu Ren, Lei Zhang, Zhengsheng Zhang and Tianyu Yang

    Citation: BMC Genomics 2020 21:141

    Content type: Research article

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  27. Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor p...

    Authors: Kashif Shahzad, Xuexian Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Meng Zhang, Bingbing Zhang, Hailin Wang, Xiuqin Qiao, Juanjuan Feng, Jianyong Wu and Chaozhu Xing

    Citation: BMC Genomics 2020 21:140

    Content type: Research article

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  28. Lead (Pb) pollution in soil has become one of the major environmental threats to plant growth and human health. Safe utilization of Pb contaminated soil by phytoremediation require Pb-tolerant rapeseed (Brassica ...

    Authors: Fugui Zhang, Xin Xiao, Kun Xu, Xi Cheng, Ting Xie, Jihong Hu and Xiaoming Wu

    Citation: BMC Genomics 2020 21:139

    Content type: Research article

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  29. Seashore paspalum (Paspalum vaginatum), a halophytic warm-seasoned perennial grass, is tolerant of many environmental stresses, especially salt stress. To investigate molecular mechanisms underlying salinity tole...

    Authors: Peipei Wu, Steven Cogill, Yijian Qiu, Zhigang Li, Man Zhou, Qian Hu, Zhihui Chang, Rooksana E. Noorai, Xiaoxia Xia, Christopher Saski, Paul Raymer and Hong Luo

    Citation: BMC Genomics 2020 21:131

    Content type: Research article

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  31. Aegilops crassa cytoplasm is an important source for investigating cytoplasmic male sterility (CMS). Moreover, the stamens of line C303A exhibit a high degree of pistillody, turning almost white. However, the mol...

    Authors: Qi Liu, Zihan Liu, Wei Li and Xiyue Song

    Citation: BMC Genomics 2020 21:124

    Content type: Research article

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  32. One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under v...

    Authors: Laura Pascual, Magdalena Ruiz, Matilde López-Fernández, Helena Pérez-Peña, Elena Benavente, José Francisco Vázquez, Carolina Sansaloni and Patricia Giraldo

    Citation: BMC Genomics 2020 21:122

    Content type: Research article

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  33. Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. Howev...

    Authors: Yunyi Zhou, Shuzhen Luo, Saba Hameed, Dong Xiao, Jie Zhan, Aiqin Wang and Longfei He

    Citation: BMC Genomics 2020 21:117

    Content type: Research article

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  34. Dunaliella salina is a good model organism for studying salt stress. In order to have a global understanding of the expression profiles of Dunaliella salina in response to hypersaline stress, we performed quantit...

    Authors: Qinghua He, Yaqiu Lin, Hong Tan, Yu Zhou, Yongli Wen, Jiajia Gan, Ruiwen Li and Qinglian Zhang

    Citation: BMC Genomics 2020 21:115

    Content type: Research article

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  35. In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, sta...

    Authors: Wilson Kimani, Li-Min Zhang, Xiao-Yuan Wu, Huai-Qing Hao and Hai-Chun Jing

    Citation: BMC Genomics 2020 21:112

    Content type: Research article

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  37. Broomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly unders...

    Authors: Zhongying Shan, Yanmiao Jiang, Haiquan Li, Jinjie Guo, Ming Dong, Jianan Zhang and Guoqing Liu

    Citation: BMC Genomics 2020 21:96

    Content type: Research article

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  38. Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is cr...

    Authors: Maria L. Irigoyen, Danielle C. Garceau, Adriana Bohorquez-Chaux, Luis Augusto Becerra Lopez-Lavalle, Laura Perez-Fons, Paul D. Fraser and Linda L. Walling

    Citation: BMC Genomics 2020 21:93

    Content type: Research article

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  39. Plant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the rboh gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of t...

    Authors: Wei Wang, Dongdong Chen, Dan Liu, Yingying Cheng, Xiaopei Zhang, Lirong Song, Mengjiao Hu, Jie Dong and Fafu Shen

    Citation: BMC Genomics 2020 21:91

    Content type: Research article

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  41. Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, t...

    Authors: Wen-Kai Hui, Fei-Yan Zhao, Jing-Yan Wang, Xiao-Yang Chen, Jue-Wei Li, Yu Zhong, Hong-Yun Li, Jun-Xing Zheng, Liang-Zhen Zhang, Qing-Min Que, Ai-Min Wu and Wei Gong

    Citation: BMC Genomics 2020 21:81

    Content type: Research article

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  42. Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing wa...

    Authors: Fernanda A. de Oliveira, Bianca B. Z. Vigna, Carla C. da Silva, Alessandra P. Fávero, Frederico P. de Matta, Ana L. S. Azevedo and Anete P. de Souza

    Citation: BMC Genomics 2020 21:78

    Content type: Research article

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  43. Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. ...

    Authors: Yating Zhang, Dong An, Changsheng Li, Zhixuan Zhao and Wenqin Wang

    Citation: BMC Genomics 2020 21:76

    Content type: Research article

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  44. Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of th...

    Authors: Man Zhang, Yanhui Liu, Qing He, Mengnan Chai, Youmei Huang, Fangqian Chen, Xiaomei Wang, Yeqiang Liu, Hanyang Cai and Yuan Qin

    Citation: BMC Genomics 2020 21:72

    Content type: Research article

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  45. Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification...

    Authors: Lanjie Zhao, Youjun Lü, Wei Chen, Jinbo Yao, Yan Li, Qiulin Li, Jingwen Pan, Shengtao Fang, Jie Sun and Yongshan Zhang

    Citation: BMC Genomics 2020 21:69

    Content type: Research article

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  46. Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implic...

    Authors: Yeyun Li, Xiaozeng Mi, Shiqi Zhao, Junyan Zhu, Rui Guo, Xiaobo Xia, Lu Liu, Shengrui Liu and Chaoling Wei

    Citation: BMC Genomics 2020 21:65

    Content type: Research article

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  47. The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many p...

    Authors: Shuting Zhang, Chen Zhu, Yumeng Lyu, Yan Chen, Zihao Zhang, Zhongxiong Lai and Yuling Lin

    Citation: BMC Genomics 2020 21:62

    Content type: Research article

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  48. Structural variations (SVs) have been reported to play an important role in genetic diversity and trait regulation. Many computer algorithms detecting SVs have recently been developed, but the use of multiple ...

    Authors: Yueyuan Liu, Mingyue Zhang, Jieying Sun, Wenjing Chang, Manyi Sun, Shaoling Zhang and Jun Wu

    Citation: BMC Genomics 2020 21:61

    Content type: Research article

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  49. Ca2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca2+ sensors, which c...

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

    Citation: BMC Genomics 2020 21:53

    Content type: Research article

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  50. Pennisetum giganteum, an abundant, fast-growing perennial C4 grass that belongs to the genus Pennisetum, family Poaceae, has been developed as a source of biomass for mushroom cultivation and production, as a sou...

    Authors: Qingyuan Li, Conglin Xiang, Lin Xu, Jinghua Cui, Shao Fu, Baolin Chen, Shoukun Yang, Pan Wang, Yanfeng Xie, Ming Wei and Zhanchang Wang

    Citation: BMC Genomics 2020 21:52

    Content type: Research article

    Published on:

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