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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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

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  35. Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bi...

    Authors: Chunmiao Shan, Chenkai Wang, Shengxiang Zhang, Yuanyuan Shi, Kelong Ma, Qingshan Yang and Jiawen Wu

    Citation: BMC Genomics 2020 21:49

    Content type: Research article

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  36. Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they e...

    Authors: Antonios Kioukis, Vassiliki A. Michalopoulou, Laura Briers, Stergios Pirintsos, David J. Studholme, Pavlos Pavlidis and Panagiotis F. Sarris

    Citation: BMC Genomics 2020 21:48

    Content type: Research article

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  37. Genomic prediction (GP) is used in animal and plant breeding to help identify the best genotypes for selection. One of the most important measures of the effectiveness and reliability of GP in plant breeding i...

    Authors: Vanda Milheiro Lourenço, Joseph Ochieng Ogutu and Hans-Peter Piepho

    Citation: BMC Genomics 2020 21:43

    Content type: Methodology Article

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  38. Light is the main source of energy and, as such, is one of the most important environmental factors for plant growth, morphogenesis, and other physiological responses. MicroRNAs (miRNAs) are endogenous non-cod...

    Authors: Fei Dong, Chuanzeng Wang, Yuhui Dong, Shuqin Hao, Lixia Wang, Xiudong Sun and Shiqi Liu

    Citation: BMC Genomics 2020 21:37

    Content type: Research article

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  39. The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F2 bulk populati...

    Authors: Moaz S. Eltahawy, Nour Ali, Imdad U. Zaid, Dalu Li, Dina Abdulmajid, Lal Bux, Hui Wang and Delin Hong

    Citation: BMC Genomics 2020 21:31

    Content type: Research article

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  40. Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circ...

    Authors: Laura Hernandez-Escribano, Erik A. Visser, Eugenia Iturritxa, Rosa Raposo and Sanushka Naidoo

    Citation: BMC Genomics 2020 21:28

    Content type: Research article

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  41. Potato virus Y (PVY) is a major pathogen of potatoes with major impact on global agricultural production. Resistance to PVY can be achieved by engineering potatoes to express a recessive, resistant allele of e...

    Authors: Pablo A. Gutierrez Sanchez, Lavanya Babujee, Helena Jaramillo Mesa, Erica Arcibal, Megan Gannon, Dennis Halterman, Molly Jahn, Jiming Jiang and Aurélie M. Rakotondrafara

    Citation: BMC Genomics 2020 21:18

    Content type: Research article

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  42. Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessi...

    Authors: Yanchao Xu, Richard Odongo Magwanga, Xiu Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Zhongli Zhou, Kunbo Wang and Fang Liu

    Citation: BMC Genomics 2020 21:15

    Content type: Research article

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  43. Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has n...

    Authors: Qi Yang, Xiaocui Niu, Xiaona Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang and Guojing Li

    Citation: BMC Genomics 2020 21:12

    Content type: Research article

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