Trends Plant Sci , IF:14.416 , 2019 Jul , V24 (7) : P602-610 doi: 10.1016/j.tplants.2019.04.002
The BAP Module: A Multisignal Integrator Orchestrating Growth.
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, 78000 Versailles, France; Universite Paris-Sud, Universite Paris-Saclay, 91405 Orsay, France.; Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, 78000 Versailles, France. Electronic address: nicolas.arnaud@inra.fr.
Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.
PMID: 31076166
New Phytol , IF:8.512 , 2019 Jul , V223 (2) : P783-797 doi: 10.1111/nph.15841
Drought resistance is mediated by divergent strategies in closely related Brassicaceae.
Institute of Network Biology (INET), Helmholtz Zentrum Munchen (HMGU), Munchen-Neuherberg, 85764, Germany.; Division of Life Science, Gyeongsang National University, Jinju, 52828, Korea.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.; VIB-UGent Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium.; UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon Cedex, 33882, France.; Microbe-Host Interactions, Ludwig-Maximilians-Universitat (LMU) Munchen, Munich, 80539, Germany.
Droughts cause severe crop losses worldwide and climate change is projected to increase their prevalence in the future. Similar to the situation for many crops, the reference plant Arabidopsis thaliana (Ath) is considered drought-sensitive, whereas, as we demonstrate, its close relatives Arabidopsis lyrata (Aly) and Eutrema salsugineum (Esa) are drought-resistant. To understand the molecular basis for this plasticity we conducted a deep phenotypic, biochemical and transcriptomic comparison using developmentally matched plants. We demonstrate that Aly responds most sensitively to decreasing water availability with early growth reduction, metabolic adaptations and signaling network rewiring. By contrast, Esa is in a constantly prepared mode as evidenced by high basal proline levels, ABA signaling transcripts and late growth responses. The stress-sensitive Ath responds later than Aly and earlier than Esa, although its responses tend to be more extreme. All species detect water scarcity with similar sensitivity; response differences are encoded in downstream signaling and response networks. Moreover, several signaling genes expressed at higher basal levels in both Aly and Esa have been shown to increase water-use efficiency and drought resistance when overexpressed in Ath. Our data demonstrate contrasting strategies of closely related Brassicaceae to achieve drought resistance.
PMID: 30955214
New Phytol , IF:8.512 , 2019 Jul , V223 (2) : P766-782 doi: 10.1111/nph.15802
A systems biology view of wood formation in Eucalyptus grandis trees submitted to different potassium and water regimes.
Laboratoire de Recherche en Sciences Vegetales, Universite de Toulouse III, CNRS, UPS, 31326, Castanet-Tolosan, France.; Max Feffer Laboratory for Plant Genetics, Department of Genetics, College of Agriculture 'Luiz de Queiroz', University of Sao Paulo, Av. Padua Dias 11, PO Box 09, Piracicaba-SP, 13418-900, Brazil.; CIRAD, UMR ECO&SOLS, F-34398, Montpellier, France.; Department of Forest Resource, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Av. Padua Dias N degrees 11, Piracicaba, Sao Paulo, 13418-900, Brazil.; CIRAD, UMR AGAP, 34395, Montpellier, Cedex 9, France.; UMR AGAP, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
Wood production in fast-growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown. E. grandis trees were submitted to four combinations of K-fertilization and water supply. Weighted gene co-expression network analysis and MixOmics-based co-regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Functional characterization of a candidate gene was performed in transgenic E. grandis hairy roots. This integrated network-based approach enabled us to identify meaningful biological processes and regulators impacted by K-fertilization and/or water limitation. It revealed that modules of co-regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade-off between biomass production and stress responses. Nested in these modules, potential new cell-wall regulators were identified, as further confirmed by the functional characterization of EgMYB137. These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co-opted by K-fertilization and/or water limitation that may potentially promote adaptive wood traits.
PMID: 30887522
Plant Biotechnol J , IF:8.154 , 2019 Jul , V17 (7) : P1261-1275 doi: 10.1111/pbi.13051
Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice.
International Rice Research Institute, Los Banos, Philippines.; Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Vic., Australia.; The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.; Food and Nutrition Research Institute (FNRI), Taguig City, Philippines.; CSIRO Health and Biosecurity, Adelaide, SA, Australia.
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wx(a) ) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.
PMID: 30549178
Cell Rep , IF:8.109 , 2019 Jul , V28 (4) : P1103-1116.e4 doi: 10.1016/j.celrep.2019.06.073
Integrating Gene and Protein Expression Reveals Perturbed Functional Networks in Alzheimer's Disease.
Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.; Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.; Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA.; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA. Electronic address: rrissman@ucsd.edu.
Asymptomatic and symptomatic Alzheimer's disease (AD) subjects may present with equivalent neuropathological burdens but have significantly different antemortem cognitive decline rates. Using the transcriptome as a proxy for functional state, we selected 414 expression profiles of symptomatic AD subjects and age-matched non-demented controls from a community-based neuropathological study. By combining brain tissue-specific protein interactomes with gene networks, we identified functionally distinct composite clusters of genes that reveal extensive changes in expression levels in AD. Global expression for clusters broadly corresponding to synaptic transmission, metabolism, cell cycle, survival, and immune response were downregulated, while the upregulated cluster included largely uncharacterized processes. We propose that loss of EGR3 regulation mediates synaptic deficits by targeting the synaptic vesicle cycle. Our results highlight the utility of integrating protein interactions with gene perturbations to generate a comprehensive framework for characterizing alterations in the molecular network as applied to AD.
PMID: 31340147
Philos Trans R Soc Lond B Biol Sci , IF:5.68 , 2019 Jul , V374 (1776) : P20180264 doi: 10.1098/rstb.2018.0264
Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies.
1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow , Glasgow G12 8QQ , UK.; 2 School of Veterinary Medicine, University College Dublin , Dublin , Ireland.; 3 Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh , Easter Bush Campus, Midlothian EH25 9RG , UK.; 6 Department of Veterinary Services, Ministry of Livestock and Fisheries, Nelson Mandela Road , Dar Es Salaam , Tanzania.; 4 Department of Infectious Diseases, University of Georgia , Athens, GA 30602 , USA.; 5 Institute of Bioinformatics, University of Georgia , Athens, GA 30602 , USA.
Livestock movements are an important mechanism of infectious disease transmission. Where these are well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities to transmission, and inform targeted surveillance and control. Here we highlight the main uses of network properties in understanding livestock disease epidemiology and discuss statistical approaches to infer network characteristics from biased or fragmented datasets. We use a 'hurdle model' approach that predicts (i) the probability of movement and (ii) the number of livestock moved to generate synthetic 'complete' networks of movements between administrative wards, exploiting routinely collected government movement permit data from northern Tanzania. We demonstrate that this model captures a significant amount of the observed variation. Combining the cattle movement network with a spatial between-ward contact layer, we create a multiplex, over which we simulated the spread of 'fast' ( R0 = 3) and 'slow' ( R0 = 1.5) pathogens, and assess the effects of random versus targeted disease control interventions (vaccination and movement ban). The targeted interventions substantially outperform those randomly implemented for both fast and slow pathogens. Our findings provide motivation to encourage routine collection and centralization of movement data to construct representative networks. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
PMID: 31104601
Cereb Cortex , IF:5.043 , 2019 Jul , V29 (7) : P3154-3167 doi: 10.1093/cercor/bhy181
Reappraisal of Interpersonal Criticism in Social Anxiety Disorder: A Brain Network Hierarchy Perspective.
Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.; Tel Aviv Center for Brain Functions, Wohl Institute for Advanced Imaging, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.; Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; The School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel.; University of California, Davis, Sacramento, CA, USA.; Department of Psychology, Stanford University, Stanford, CA, USA.; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Emotion regulation is thought to involve communication between and within large-scale brain networks that underlie emotion reactivity and cognitive control. Aberrant network interaction might therefore be a key neural feature of mental disorders that involve emotion dysregulation. Here we tested whether connectivity hierarchies within and between emotion reactivity and cognitive reappraisal networks distinguishes social anxiety disorder (SAD) patients (n = 70) from healthy controls (HC) (n = 25). To investigate network organization, we implemented a graph-theory method called Dependency Network Analysis. Participants underwent fMRI while watching or reappraising video clips involving interpersonal verbal criticism. During reappraisal, the reappraisal network exerted less influence on the reactivity network in SAD participants. Specifically, the influence of the right inferior frontal gyrus on both reappraisal and reactivity networks was significantly reduced in SAD compared with HC, and correlated negatively with negative emotion ratings among SAD participants. Surprisingly, the amygdala exhibited reduced influence on the reappraisal network in SAD relative to HC. Yet, during the watch condition, the left amygdala's influence on the reactivity network increased with greater social anxiety symptoms among SAD participants. These findings refine our understanding of network organization that contributes to efficient reappraisal or to disturbances in applying this strategy in SAD.
PMID: 30124815
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (14) doi: 10.3390/ijms20143480
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize.
Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China.; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China.; Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China. wanxiangyuan@ustb.edu.cn.; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China. wanxiangyuan@ustb.edu.cn.
The "competing endogenous RNA (ceRNA) hypothesis" has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potentially novel microRNAs (miRNAs) were identified from the transcriptomes. Predicted ceRNAs and target genes were found to conserve in sequences of recognition sites where their corresponding miRNAs bound. We then reconstructed 79 ceRNA-miRNA-target gene regulatory networks consisting of 51 known miRNAs, 28 potentially novel miRNAs, 619 ceRNA-miRNA pairs, and 869 miRNA-target gene pairs. More than half of the regulation pairs showed significant negative correlations at transcriptional levels. Several well-studied miRNA-target gene pairs associated with plant flower development were located in some networks, including miR156-SPL, miR159-MYB, miR160-ARF, miR164-NAC, miR172-AP2, and miR319-TCP pairs. Six target genes in the networks were found to be orthologs of functionally confirmed genes participating in anther development in plants. Our results provide an insight that the ceRNA-miRNA-target gene regulatory networks likely contribute to anther development in maize. Further functional studies on a number of ceRNAs, miRNAs, and target genes will facilitate our deep understanding on mechanisms of anther development and sexual plants reproduction.
PMID: 31311189
Tree Physiol , IF:3.655 , 2019 Jul , V39 (7) : P1159-1172 doi: 10.1093/treephys/tpz025
Transcription factors involved in the regulatory networks governing the Calvin-Benson-Bassham cycle.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Transcription factors (TFs) play crucial roles in the regulation of photosynthesis; elucidating these roles will facilitate our understanding of photosynthesis and thus accelerate its improvement for enhancing crop yield. Promoter analysis of 52 nuclear-encoded Populus tomentosa Carr. genes involved in the Calvin-Benson-Bassham (CBB) cycle revealed 706 motifs and 326 potentially interacting TFs. A backward elimination random forest (BWERF) algorithm reduced the number of TFs to 40, involved in a three-layer gene regulatory network (GRN) including 46 photosynthesis genes (bottom layer), 25 TFs (second layer) and 15 TFs (top layer). Phenotype-genotype association identified 248 single-nucleotide polymorphisms (SNPs) within 72 genes associated with 11 photosynthesis traits. Of the regulatory pairs identified by the BWERF (202 pairs), 77 TF-target combinations harbored SNPs associated with the same trait, supporting similar mechanisms of phenotype modulation. We used expression quantitative trait nucleotide (eQTN) analysis to identify causal SNPs affecting gene expression, identifying 1851 eQTN signals for 50 eGenes (genes whose expressions are regulated by eQTNs). Distribution patterns identified 14 eQTNs from seven TFs associated with eight expression levels of their downstream targets (defined in the GRN), whereas seven TF-target pairs were also identified by phenotype-genotype associations. To further validate the roles of TFs at the metabolic level, we selected 6764 SNPs from 55 genes (identified by GRN-association or GRN-eQTN pairs or both) for metabolic association, identifying variants within 10 TFs affecting metabolic processes underlying the CBB cycle. Our study provides new insights into the photosynthesis pathway in poplar and may facilitate understanding of processes underlying photosynthesis improvement.
PMID: 30941430
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P574 doi: 10.1186/s12864-019-5945-1
Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize.
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China.; College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China.; College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China.; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China. wengjianfeng@caas.cn.; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China. lixinhai@caas.cn.
BACKGROUND: Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. RESULTS: Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. CONCLUSION: Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm.
PMID: 31296166
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P564 doi: 10.1186/s12864-019-5910-z
Identification and differential expression analysis of anthocyanin biosynthetic genes in leaf color variants of ornamental kale.
Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P. R. China, Beijing, 100097, China.; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P. R. China, Beijing, 100097, China. liufan@nercv.org.
BACKGROUND: Anthocyanins perform diverse biological functions in plants and are beneficial to human health. Leaf color is the most important trait of ornamental kale and the characteristics of changes in leaf color make it an ideal material to elucidate genetic mechanisms of anthocyanins accumulation in Brassica oleracea. To elucidate the anthocyanin distribution, metabolic profiles and differentially expressed anthocyanin biosynthetic genes between different colored accessions can pave the way for understanding the genetic regulatory mechanisms of anthocyanin biosynthesis and accumulation in ornamental kale. RESULTS: In this study, anthocyanin distributions in red- and white-leaved ornamental kale accessions were determined. Thirty-four anthocyanins were detected in the red-leaved accession. The complete set of anthocyanin biosynthetic genes in the B. oleracea reference genome was identified and differential expression analysis based on RNA-seq was conducted. Eighty-one anthocyanin biosynthetic genes were identified in the B. oleracea reference genome. The expression patterns and differential expressions of these genes in different leaf types indicated that late biosynthetic genes (BoDFR1, BoANS1 and 2, and BoUGT79B1.1), positive regulatory genes (BoTTG1, BoTT8, and Bol012528), a negative regulatory gene (BoMYBL2.1), and transport genes (BoTT19.1 and BoTT19.2) may play roles in anthocyanin accumulation in ornamental kale. A genetic regulatory network of anthocyanin accumulation in ornamental kale was constructed. CONCLUSIONS: The distribution of pigments and anthocyanin profiles explained the leaf color phenotypes of ornamental kales. The identification of key genes and construction of genetic regulatory network in anthocyanin accumulation in ornamental kale elucidated the genetic basis of leaf color variants. These findings enhance the understanding of the genetic mechanisms and regulatory network of anthocyanin accumulation in B. oleracea, and provide a theoretical basis for breeding new cultivars of Brassica vegetables with enhanced ornamental and nutritional value.
PMID: 31286853
BMC Plant Biol , IF:3.497 , 2019 Jul , V19 (1) : P313 doi: 10.1186/s12870-019-1908-6
Time-series transcriptome provides insights into the gene regulation network involved in the volatile terpenoid metabolism during the flower development of lavender.
Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China.; College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, China. hfwang@bjfu.edu.cn.; Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China. cuihongxia@ibcas.ac.cn.; Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, 100093, China. shilei_67@126.com.
BACKGROUND: Essential oils (EOs) of Lavandula angustifolia, mainly consist of monoterpenoids and sesquiterpenoids, are of great commercial value. The multi-flower spiciform thyrse of lavender not only determines the output of EOs but also reflects an environmental adaption strategy. With the flower development and blossom in turn, the fluctuation of the volatile terpenoids displayed a regular change at each axis. However, the molecular mechanism underlying the regulation of volatile terpenoids during the process of flowering is poorly understood in lavender. Here, we combine metabolite and RNA-Seq analyses of flowers of five developmental stages at first- and second-axis (FFDSFSA) and initial flower bud (FB0) to discover the active terpenoid biosynthesis as well as flowering-related genes. RESULTS: A total of 56 mono- and sesquiterpenoids were identified in the EOs of L. angustifolia 'JX-2'. FB0' EO consists of 55 compounds and the two highest compounds, beta-trans-ocimene (20.57%) and (+)-R-limonene (17.00%), can get rid of 74.71 and 78.41% aphids in Y-tube olfactometer experiments, respectively. With sequential and successive blossoms, temporally regulated volatiles were linked to pollinator attraction in field and olfaction bioassays. In three characteristic compounds of FFDSFSA' EOs, linalyl acetate (72.73%) and lavandulyl acetate (72.09%) attracted more bees than linalool (45.35%). Many transcripts related to flowering time and volatile terpenoid metabolism expressed differently during the flower development. Similar metabolic and transcriptomic profiles were observed when florets from the two axes were maintained at the same maturity grade. Besides both compounds and differentially expressed genes were rich in FB0, most volatile compounds were significantly correlated with FB0-specific gene module. Most key regulators related to flowering and terpenoid metabolism were interconnected in the subnetwork of FB0-specific module, suggesting the cross-talk between the two biological processes to some degree. CONCLUSIONS: Characteristic compounds and gene expression profile of FB0 exhibit ecological value in pest control. The precise control of each-axis flowering and regular emissions at transcriptional and metabolic level are important to pollinators attraction for lavender. Our study sheds new light on lavender maximizes its fitness from "gene-volatile terpenoid-insect" three layers.
PMID: 31307374
BMC Vet Res , IF:1.835 , 2019 Jul , V15 (1) : P262 doi: 10.1186/s12917-019-1962-1
Network analysis of dairy cattle movement and associations with bovine tuberculosis spread and control in emerging dairy belts of Ethiopia.
National Animal Health Diagnostic and Investigation Center, P. O. Box 04, Sebeta, Ethiopia. getnet.abie.mekonnen@gmail.com.; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia. getnet.abie.mekonnen@gmail.com.; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia.; Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.; Bacteriology Department, Animal and Plant Health Agency, Surrey, KT15 3NB, UK.
BACKGROUND: Dairy cattle movement could be a major risk factor for the spread of bovine tuberculosis (BTB) in emerging dairy belts of Ethiopia. Dairy cattle may be moved between farms over long distances, and hence understanding the route and frequency of the movements is essential to establish the pattern of spread of BTB between farms, which could ultimately help to inform policy makers to design cost effective control strategies. The objective of this study was, therefore, to investigate the network structure of dairy cattle movement and its influence on the transmission and prevalence of BTB in three emerging areas among the Ethiopian dairy belts, namely the cities of Hawassa, Gondar and Mekelle. METHODS: A questionnaire survey was conducted in 278 farms to collect data on the pattern of dairy cattle movement for the last 5 years (September 2013 to August 2018). Visualization of the network structure and analysis of the relationship between the network patterns and the prevalence of BTB in these regions were made using social network analysis. RESULTS: The cattle movement network structure display both scale free and small world properties implying local clustering with fewer farms being highly connected, at higher risk of infection, with the potential to act as super spreaders of BTB if infected. Farms having a history of cattle movements onto the herds were more likely to be affected by BTB (OR: 2.2) compared to farms not having a link history. Euclidean distance between farms and the batch size of animals moved on were positively correlated with prevalence of BTB. On the other hand, farms having one or more outgoing cattle showed a decrease on the likelihood of BTB infection (OR = 0.57) compared to farms which maintained their cattle. CONCLUSION: This study showed that the patterns of cattle movement and size of animal moved between farms contributed to the potential for BTB transmission. The few farms with the bulk of transmission potential could be efficiently targeted by control measures aimed at reducing the spread of BTB. The network structure described can also provide the starting point to build and estimate dynamic transmission models for BTB, and other infectious diseases.
PMID: 31349832