Trends Plant Sci , IF:14.416 , 2020 Nov , V25 (11) : P1154-1170 doi: 10.1016/j.tplants.2020.05.009
Altering Plant Architecture to Improve Performance and Resistance.
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.; The Unidad de Genomica Avanzada (Langebio), Centro de Investigacion y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico; Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, TX, USA.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. Electronic address: caodong@caas.cn.; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam; Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. Electronic address: tranplamson@duytan.edu.vn.
High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.
PMID: 32595089
Bioresour Technol , IF:7.539 , 2020 Nov , V316 : P123823 doi: 10.1016/j.biortech.2020.123823
Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting.
State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.; Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, Illinois, USA.; Taian Soil and Fertilizer Workstation, Tai'an 271000, China.; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an 271018, China.; College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an 271018, China. Electronic address: zhoubo2798@163.com.
In this study, green soybean hulls and maize straw were used for composting to explore the dynamics of material conversion, bacterial and fungal communities and metabolic functions. The results showed that bacterial and fungal communities had different temporal successions during composting. The bacterium Streptosporangiaceae was a biomarker in the thermophilic stage of composting, and the fungus Chaetomiaceae was a biomarker in the thermophilic stage and cooling stage. In the bacterial network, the germination index (GI) had a time-delayed association with Truepera, Pseudomonas and Methylococcaceae, which represented the key physicochemical characteristics that affect the community. In the fungal community, the GI, pH, fulvic acid (FA) and temperature etc. had a joint effect. Carbohydrate metabolism and amino acid metabolism were the main metabolic pathways, and saprotrophs represented the dominant fungal trophic mode in the composting process. These results provide a reference from screening specific and efficient agents to accelerate natural vegetable composting.
PMID: 32795866
Plant J , IF:6.141 , 2020 Nov , V104 (3) : P812-827 doi: 10.1111/tpj.14961
CropPAL for discovering divergence in protein subcellular location in crops to support strategies for molecular crop breeding.
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia.; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.; Robinson Research Institute and Adelaide Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.; University Library, The University of Western Australia, Crawley, WA, 6009, Australia.
Agriculture faces increasing demand for yield, higher plant-derived protein content and diversity while facing pressure to achieve sustainability. Although the genomes of many of the important crops have been sequenced, the subcellular locations of most of the encoded proteins remain unknown or are only predicted. Protein subcellular location is crucial in determining protein function and accumulation patterns in plants, and is critical for targeted improvements in yield and resilience. Integrating location data from over 800 studies for 12 major crop species into the cropPAL2020 data collection showed that while >80% of proteins in most species are not localised by experimental data, combining species data or integrating predictions can help bridge gaps at similar accuracy. The collation and integration of over 61 505 experimental localisations and more than 6 million predictions showed that the relative sizes of the protein catalogues located in different subcellular compartments are comparable between crops and Arabidopsis. A comprehensive cross-species comparison showed that between 50% and 80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the phylogenetic relationship of the species. Protein subcellular locations in major biosynthesis pathways are more often conserved than in metabolic pathways. Underlying this conservation is a clear potential for subcellular diversity in protein location between species by means of gene duplication and alternative splicing. Our cropPAL data set and search platform (https://crop-pal.org) provide a comprehensive subcellular proteomics resource to drive compartmentation-based approaches for improving yield, protein composition and resilience in future crop varieties.
PMID: 32780488
J Ginseng Res , IF:5.487 , 2020 Nov , V44 (6) : P757-769 doi: 10.1016/j.jgr.2019.05.009
Metabolomes and transcriptomes revealed the saponin distribution in root tissues of Panax quinquefolius and Panax notoginseng.
Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.; Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China.; Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China.; Institute of Sanqi Research, Wenshan University, Wenshan, China.; Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai, China.
Background: Panax quinquefolius and Panax notoginseng are widely used and well known for their pharmacological effects. As main pharmacological components, saponins have different distribution patterns in the root tissues of Panax plants. Methods: In this study, the representative ginsenosides were detected and quantified by desorption electrospray ionization mass spectrometry and high-performance liquid chromatography analysis to demonstrate saponin distribution in the root tissues of P. quinquefolius and P. notoginseng, and saponin metabolite profiles were analyzed by metabolomes to obtain the biomarkers of different root tissues. Finally, the transcriptome analysis was performed to demonstrate the molecular mechanisms of saponin distribution by gene profiles. Results: There was saponin distribution in the root tissues differed between P. quinquefolius and P. notoginseng. Eight-eight and 24 potential biomarkers were detected by metabolome analysis, and a total of 340 and 122 transcripts involved in saponin synthesis that were positively correlated with the saponin contents (R > 0.6, P < 0.05) in the root tissues of P. quinquefolius and P. notoginseng, respectively. Among them, GDPS1, CYP51, CYP64, and UGT11 were significantly correlated with the contents of Rg1, Re, Rc, Rb2, and Rd in P. quinquefolius. UGT255 was markedly related to the content of R1; CYP74, CYP89, CYP100, CYP103, CYP109, and UGT190 were markedly correlated with the Rd content in P. notoginseng. Conclusions: These results provided the visual and quantitative profiles of and confirmed the pivotal transcripts of CYPs and UGTs regulating the saponin distribution in the root tissues of P. quinquefolius and P. notoginseng.
PMID: 33192118
FEMS Microbiol Ecol , IF:3.675 , 2020 Nov doi: 10.1093/femsec/fiaa222
Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum.
Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens, Greece.; Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (1) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (2) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.
PMID: 33155054
BMC Plant Biol , IF:3.497 , 2020 Nov , V20 (1) : P528 doi: 10.1186/s12870-020-02735-3
Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum).
State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China.; School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.; State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China. txia@qlu.edu.cn.; School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China. txia@qlu.edu.cn.
BACKGROUND: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered. RESULTS: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a 'blue' module highly associated with cellulose synthesis and a 'turquoise' module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes. CONCLUSIONS: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.
PMID: 33213376
J Pharm Biomed Anal , IF:3.209 , 2020 Nov , V191 : P113614 doi: 10.1016/j.jpba.2020.113614
Network analysis, chemical characterization, antioxidant and enzyme inhibitory effects of foxglove (Digitalis cariensis Boiss. ex Jaub. & Spach): A novel raw material for pharmaceutical applications.
Department of Biology, Faculty of Science, Selcuk University, Campus, Konya, Turkey. Electronic address: biyologzengin@yahoo.com.; Department of Biology, Faculty of Science, Selcuk University, Campus, Konya, Turkey.; Erciyes University Halil Bayraktar Health Services Vocational College, Kayseri, Turkey; Drug Application and Research Center, Erciyes University, Kayseri, Turkey.; Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, 230 Reduit, Mauritius. Electronic address: f.mahomoodally@uom.ac.mu.; Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, 230 Reduit, Mauritius.; Agricultural and Molecular Research and Service Institute, University of Nyiregyhaza, Nyiregyhaza, Hungary(e).; Chitkara College of Pharmacy, Chitkara University, Punjab, India.; Department of Pharmacy, "G. d'Annunzio University" Chieti-Pescara, Via dei Vestini n. 31, 66100 Chieti, Italy.
The present study outlines the phenolic composition and pharmacological properties of different extracts of Digitalis cariensis Boiss. ex Jaub. & Spach root and aerial parts. The metabolic profiles of the studied extracts were characterized by UHPLC-MS. The in vitro antioxidant and enzyme (acetylcholinesterase (AChE), butyrylcholinesterase (BChE), tyrosinase, alpha-amylase, and alpha-glucosidase) inhibitory potential of the extracts were determined. Bioinformatics and docking investigations were also conducted to support the enzyme inhibition test and predict putative targets for potential pharmacological applications. Overall, the methanolic extract followed by the water extract of the D. cariensis root were found to be superior source of antioxidant compounds except for metal chelating ability, in which the water extract of the root (26.34 +/- 1.54 mg EDTAE/g) and aerial parts (16.47 +/- 0.88 mg EDTAE/g) have showed the highest activity. The tested extracts were potent against AChE (9.11 +/- 0.27-9.79 +/- 0.28 mg GEs/g extract), alpha-amylase (0.12 +/- 0.01- 0.50 +/- 0.01 mmol ACEs/g extract) and alpha-glucosidase (0.28 +/- 0.01-17.29 +/- 0.24 mmol ACEs/ g extract). Notable activity against tyrosinase was displayed by the methanolic extracts (Root-MeOH: 123.71 +/- 2.70 and aerial parts - MeOH: 137.96 +/- 1.07 mg KAE/g extract), while none of the extracts were potent against BChE. According to docking investigations, the observed anti-tyrosinase effect could be related, at least partially, to the presence of luteolin, rosmarinic acid and kaempferol in the extracts. Results amassed herein is the first report on the biological attributes of D. cariensis, which validate the pharmacological uses of this plant.
PMID: 32980793
J Appl Microbiol , IF:3.066 , 2020 Nov doi: 10.1111/jam.14927
Application of a microbial consortium improves the growth of Camellia sinensis and influences the indigenous rhizosphere bacterial communities.
Tea Research Institute of Chongqing Academy of Agricultural Science, Chongqing, China.; Vegetable Technical Extension Station, Qingpu District Shanghai, Shanghai, China.
AIMS: To investigate the role of a microbial consortium in influencing of Camellia sinensis growth and rhizosphere bacteria microbial community structure. METHODS AND RESULTS: Based on glasshouse trials, the microbial consortium TCM was selected for a field trial. TCM significantly increased bud density (67.53%), leaf area (31.15%) and hundred-bud weight (22.5%) compared with the control treatment (P < 0.01) during 180 days. Furthermore, TCM-treated soil showed a significant increase (P < 0.05) in organic matter (60.89%), total nitrogen (66.22%), total phosphorus (3.34%), available phosphorus (3.82%), available potassium (9.24%) and 2-3 mm water-stable aggregates (77.93%). Molecular ecological network analysis of the rhizobacteria indicated an increase in modularity and the number of community, connection and nodes after TCM application. Several plant growth-promoting bacteria were categorized as hubs or indicators, such as Haliangium, Catenulispora and Gemmatimonas, and showed intensive connections with other bacteria. CONCLUSIONS: The TCM consortium enhances the effectiveness of soil mineral nutrition, influences the indigenous rhizobacterial community, alters the rhizobacterial network structure in the rhizosphere and promotes the growth of C. sinensis. SIGNIFICANCE AND IMPACT OF THE STUDY: The TCM growth-promoting mechanism was closely related to rhizosphere bacterial diversity; therefore, strengthening rhizobacterial interactions may help promote C. sinensis growth, which could be a sustainable approach for improving C. sinensis growth and health in tea plantations.
PMID: 33170985
G3 (Bethesda) , IF:2.781 , 2020 Nov , V10 (11) : P4215-4226 doi: 10.1534/g3.120.401477
Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana.
Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands margi.hartanto@wur.nl harm.nijveen@wur.nl.; Laboratory of Plant Physiology, Wageningen University, NL-6708 PB Wageningen, The Netherlands.; Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands.; Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands.; Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands.
Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTL in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
PMID: 32963085
Genome , IF:2.037 , 2020 Nov , V63 (11) : P561-575 doi: 10.1139/gen-2020-0041
Identification of potential proteases for abdominal aortic aneurysm by weighted gene coexpression network analysis.
Department of Vascular Surgery, Peking Union Medical College Hospital, Beijing 100730, P.R. China.; Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China.
Proteases are involved in the degradation of the extracellular matrix (ECM), which contributes to the formation of abdominal aortic aneurysm (AAA). To identify new disease targets in addition to the results of previous microarray studies, we performed next-generation sequencing (NGS) of the whole transcriptome of Angiotensin II-treated ApoE(-/-) male mice (n = 4) and control mice (n = 4) to obtain differentially expressed genes (DEGs). Identified DEGs of proteases were analyzed using weighted gene coexpression network analysis (WGCNA). RT-qPCR was conducted to validate the differential expression of selected hub genes. We found that 43 DEGs were correlated with the expression of the protease profile, and most were clustered in immune response module. Among 26 hub genes, we found that Mmp16 and Mmp17 were significantly downregulated in AAA mice, while Ctsa, Ctsc, and Ctsw were upregulated. Our functional annotation analysis of genes coexpressed with the five hub genes indicated that Ctsw and Mmp17 were involved in T cell regulation and Cell adhesion molecule pathway, respectively, and that both were involved in general regulation of the cell cycle and gene expression. Overall, our data suggest that these ectopic genes are potentially crucial to AAA formation and may act as biomarkers for the diagnosis of AAA.
PMID: 32783773
Heliyon , 2020 Nov , V6 (11) : Pe05328 doi: 10.1016/j.heliyon.2020.e05328
Structural characterization of stripe rust progress in wheat crops sown at different planting dates.
Plant Protection Research Department, Kermanshah Agricultural & Natural Resources Research & Education Center, Iran.; Iranian Research Institute of Plant Protection, Iran.
An advanced insight into characterizing stripe rust progress curves is required to improve accuracy and efficiency of future research for disease measurement and estimation purposes. The rate of stripe rust increase in wheat crops is highly variable, resulting in variations and uncertainties in evaluating disease progress over time. This variability was described by fitting standard curves to disease severity data collected over a four-season experiment to identify effective disease curve elements in Iranian wheat cultivars planted at different dates. Gaussian curves appeared to be the best fitted models for all four growing seasons. Three Gaussian parameters in combination with the area under the disease progress curve (AUDPC), disease onset time, maximum disease incidence and severity were then considered to describe the rate of disease increase. Based on H-tests of Kruskal-Wallis one-way analysis of variance, cultivar and planting date significantly affected AUDPC, maximum disease incidence and severity. There were significant correlations between continuous disease descriptors. Then, significant associations were determined between AUDPC, disease onset time, Gaussian parameters, maximum disease incidence and severity according to factor analysis. With these novel findings, we should be aware of descriptive value of wheat-stripe-rust progress variables. Such information will assist with stripe rust measurements for wheat breeding programs, yield loss estimation, development of disease control strategy, and epidemiological studies.
PMID: 33241134
J Integr Bioinform , 2020 Nov doi: 10.1515/jib-2020-0029
To the question of the digital platform "bioinformatics" creating and its system-forming solutions.
The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.; Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia.
The article reports the main provisions of the concept and solutions for creating the digital platform in the field of bioinformatics and the formation of the thematically oriented and industrial digital ecosystems on its basis. The composition and structure of the digital platform are discussed: information repositories, data and knowledge bases, thematically oriented software repository, task-oriented services for various target groups of users. Within the framework of the platform, it is also planned to organize a system of high-quality access to specialized data centres and high-performance computing infrastructure. Particular attention is devoted to one of the components of such platform - the project office for bioresource collections management. The project office has registered such types of collections as animal collections: wild and laboratory animals, live breeding, museum zoological animal collections, farm animals; plant collections: herbarium funds of plants biological diversity, living collections of natural flora, agricultural plants. Collection types such as collections of human biomaterials, cell culture collections, microorganism collections are important for medical research.
PMID: 33141107