1
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Tsujimoto H, Adelman ZN. An 11-point time course midgut transcriptome across 72 h after bloodfeeding provides detailed temporal resolution of transcript expression in the arbovirus vector, Aedes aegypti. Genome Res 2023; 33:1638-1648. [PMID: 37802532 PMCID: PMC10620042 DOI: 10.1101/gr.277808.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023]
Abstract
As the major vector for dengue, Zika, yellow fever, and chikungunya viruses, the mosquito Aedes aegypti is one of the most important insects in public health. These viruses are transmitted by bloodfeeding, which is also necessary for the reproduction of the mosquito. Thus, the midgut plays an essential role in mosquito physiology as the center for bloodmeal digestion and as an organ that serves as the first line of defense against viruses. Despite its importance, transcriptomic dynamics with fine temporal resolution across the entire digestion cycle have not yet been reported. To fill this gap, we conducted a transcriptomic analysis of A. aegypti female midguts across a 72-h bloodmeal digestion cycle for 11 time points, with a particular focus on the first 24 h. PCA analysis confirmed that 72 h is indeed a complete digestion cycle. Cluster and GO enrichment analysis showed the orchestrated modulation of thousands of genes to accomplish the midgut's role as the center for digestion, as well as nutrient transport with a clear progression with sequential emphasis on transcription, translation, energy production, nutrient metabolism, transport, and finally, autophagy by 24-36 h. We further determined that many serine proteases are robustly expressed as if to prepare for unexpected physiological challenges. This study provides a powerful resource for the analysis of genomic features that coordinate the rapid and complex transcriptional program induced by mosquito bloodfeeding.
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Affiliation(s)
- Hitoshi Tsujimoto
- Department of Entomology and Texas A&M Agrilife Research, College Station, Texas 77853, USA
| | - Zach N Adelman
- Department of Entomology and Texas A&M Agrilife Research, College Station, Texas 77853, USA
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2
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Vu HTH, Zhang Y, Tuteja G, Dorman KS. Unsupervised contrastive peak caller for ATAC-seq. Genome Res 2023; 33:1133-1144. [PMID: 37217250 PMCID: PMC10538491 DOI: 10.1101/gr.277677.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023]
Abstract
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling." Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. Raw coverage data are encoded to obtain low-dimensional embeddings and optimized to minimize a contrastive loss over biological replicates. These embeddings are passed to another contrastive loss for learning and predicting peaks and decoded to denoised data under an autoencoder loss. We compared our replicative contrastive learner (RCL) method with other existing methods on ATAC-seq data, using annotations from ChromHMM genomic labels and transcription factor ChIP-seq as noisy truth. RCL consistently achieved the best performance.
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Affiliation(s)
- Ha T H Vu
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
| | - Yudi Zhang
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Geetu Tuteja
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
| | - Karin S Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA;
- Department of Genetics, Development and Cell Biology, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
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3
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Shrestha S, Fu Y, Michael VN, Meru G. Whole Genome Re-sequencing and Bulk Segregant Analysis Reveals Chromosomal Location for Papaya Ringspot Virus W Resistance in Squash. Front Plant Sci 2022; 13:848631. [PMID: 35665151 PMCID: PMC9161299 DOI: 10.3389/fpls.2022.848631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/07/2022] [Indexed: 06/15/2023]
Abstract
Squash (Cucurbita moschata) is among the most important cucurbit crops grown worldwide. Plant pathogen, Papaya ringspot virus W (PRSV-W) causes significant yield loss in commercial squash production globally. The development of virus-resistant cultivars can complement integrated disease management and mitigate losses due to viral infections. However, the genetic loci and molecular markers linked to PRSV-W resistance that could facilitate marker-assisted selection (MAS) for accelerated cultivar development are unknown. In this study, quantitative trait loci (QTL), molecular markers, and candidate genes associated with PRSV-W resistance in squash were identified in an F2 population (n = 118) derived from a cross between Nigerian Local accession (resistant) and Butterbush cultivar (susceptible). Whole genome re-sequencing-based bulked segregant analysis (QTLseq method; n = 10 for each bulk) and non-parametric interval mapping were used to identify a major QTL associated with PRSV-W resistance on chromosome 9 (QtlPRSV-C09) (p < 0.05) of C. moschata. QtlPRSV-C09 extended from 785,532 to 5,093,314 bp and harbored 12,245 SNPs among which 94 were high-effect variants. To validate QtlPRSV-C09, 13 SNP markers were assayed as Kompetitive allele-specific PCR (KASP) markers in the F2 population and tested for the association with PRSV-W resistance. Among these, two KASP markers (Ch09_2080834 and Ch09_5023865-1) showed significant association with PRSV-W resistance (p < 0.05). The two SNPs were located within exons of putative disease-resistant genes encoding the clathrin assembly family and actin cytoskeleton-regulatory complex proteins, which are implicated in disease resistance across plant species. The findings of this study will facilitate MAS for PRSV-W resistance in squash and allow further understanding of the functional mechanisms underlying potyvirus resistance in Cucurbita species.
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4
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Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Res 2022; 32:791-804. [PMID: 35361626 PMCID: PMC8997358 DOI: 10.1101/gr.276027.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 02/28/2022] [Indexed: 11/24/2022]
Abstract
An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold the key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated data set, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.
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Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sung Bong Shin
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
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5
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Kud J, Pillai SS, Raber G, Caplan A, Kuhl JC, Xiao F, Dandurand LM. Belowground Chemical Interactions: An Insight Into Host-Specific Behavior of Globodera spp. Hatched in Root Exudates From Potato and Its Wild Relative, Solanum sisymbriifolium. Front Plant Sci 2022; 12:802622. [PMID: 35095973 PMCID: PMC8791010 DOI: 10.3389/fpls.2021.802622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Understanding belowground chemical interactions between plant roots and plant-parasitic nematodes is immensely important for sustainable crop production and soilborne pest management. Due to metabolic diversity and ever-changing dynamics of root exudate composition, the impact of only certain molecules, such as nematode hatching factors, repellents, and attractants, has been examined in detail. Root exudates are a rich source of biologically active compounds, which plants use to shape their ecological interactions. However, the impact of these compounds on nematode parasitic behavior is poorly understood. In this study, we specifically address this knowledge gap in two cyst nematodes, Globodera pallida, a potato cyst nematode and the newly described species, Globodera ellingtonae. Globodera pallida is a devastating pest of potato (Solanum tuberosum) worldwide, whereas potato is a host for G. ellingtonae, but its pathogenicity remains to be determined. We compared the behavior of juveniles (J2s) hatched in response to root exudates from a susceptible potato cv. Desirée, a resistant potato cv. Innovator, and an immune trap crop Solanum sisymbriifolium (litchi tomato - a wild potato relative). Root secretions from S. sisymbriifolium greatly reduced the infection rate on a susceptible host for both Globodera spp. Juvenile motility was also significantly influenced in a host-dependent manner. However, reproduction on a susceptible host from juveniles hatched in S. sisymbriifolium root exudates was not affected, nor was the number of encysted eggs from progeny cysts. Transcriptome analysis by using RNA-sequencing (RNA-seq) revealed the molecular basis of root exudate-mediated modulation of nematode behavior. Differentially expressed genes are grouped into two major categories: genes showing characteristics of effectors and genes involved in stress responses and xenobiotic metabolism. To our knowledge, this is the first study that shows genome-wide root exudate-specific transcriptional changes in hatched preparasitic juveniles of plant-parasitic nematodes. This research provides a better understanding of the correlation between exudates from different plants and their impact on nematode behavior prior to the root invasion and supports the hypothesis that root exudates play an important role in plant-nematode interactions.
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Affiliation(s)
- Joanna Kud
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, United States
| | | | - Gabriel Raber
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, United States
| | - Allan Caplan
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - Joseph C. Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - Louise-Marie Dandurand
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, United States
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6
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Ghodhbane-Gtari F, D’Angelo T, Gueddou A, Ghazouani S, Gtari M, Tisa LS. Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules. Front Microbiol 2021; 12:749760. [PMID: 34925263 PMCID: PMC8674757 DOI: 10.3389/fmicb.2021.749760] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/08/2021] [Indexed: 02/01/2023] Open
Abstract
Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.
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Affiliation(s)
- Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université de la Manouba, Sidi Thabet, Tunisia
- Unité de Bactériologie Moléculaire et Génomique, Centre Urbain Nord, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| | - Timothy D’Angelo
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Abdellatif Gueddou
- Unité de Bactériologie Moléculaire et Génomique, Centre Urbain Nord, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| | - Sabrine Ghazouani
- Unité de Bactériologie Moléculaire et Génomique, Centre Urbain Nord, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
- Unité de Bactériologie Moléculaire et Génomique, Centre Urbain Nord, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
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7
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Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O. The genomic basis of evolutionary differentiation among honey bees. Genome Res 2021; 31:1203-1215. [PMID: 33947700 PMCID: PMC8256857 DOI: 10.1101/gr.272310.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
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Affiliation(s)
- Bertrand Fouks
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California 95161, USA
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Hung N Nguyen
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jacob Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Daniel Ence
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Katharina J Hoff
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Stefanie Nachweide
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Lars Romoth
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Mario Stanke
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | | | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nikolaus Koeniger
- Department of Behavioral Physiology and Sociobiology (Zoology II), University of Würzburg, 97074 Würzburg, Germany
| | - Panuwan Chantawannakul
- Environmental Science Research Center (ESRC) and Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gene E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christine G Elsik
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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8
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Valle D, Shimizu G, Izbicki R, Maracahipes L, Silverio DV, Paolucci LN, Jameel Y, Brando P. The Latent Dirichlet Allocation model with covariates (LDAcov): A case study on the effect of fire on species composition in Amazonian forests. Ecol Evol 2021; 11:7970-7979. [PMID: 34188865 PMCID: PMC8216892 DOI: 10.1002/ece3.7626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 11/06/2022] Open
Abstract
Understanding and predicting the effect of global change phenomena on biodiversity is challenging given that biodiversity data are highly multivariate, containing information from tens to hundreds of species in any given location and time. The Latent Dirichlet Allocation (LDA) model has been recently proposed to decompose biodiversity data into latent communities. While LDA is a very useful exploratory tool and overcomes several limitations of earlier methods, it has limited inferential and predictive skill given that covariates cannot be included in the model. We introduce a modified LDA model (called LDAcov) which allows the incorporation of covariates, enabling inference on the drivers of change of latent communities, spatial interpolation of results, and prediction based on future environmental change scenarios. We show with simulated data that our approach to fitting LDAcov is able to estimate well the number of groups and all model parameters. We illustrate LDAcov using data from two experimental studies on the long-term effects of fire on southeastern Amazonian forests in Brazil. Our results reveal that repeated fires can have a strong impact on plant assemblages, particularly if fuel is allowed to build up between consecutive fires. The effect of fire is exacerbated as distance to the edge of the forest decreases, with small-sized species and species with thin bark being impacted the most. These results highlight the compounding impacts of multiple fire events and fragmentation, a scenario commonly found across the southern edge of Amazon. We believe that LDAcov will be of wide interest to scientists studying the effect of global change phenomena on biodiversity using high-dimensional datasets. Thus, we developed the R package LDAcov to enable the straightforward use of this model.
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Affiliation(s)
- Denis Valle
- School of Forest, Fisheries, and Geomatics SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Gilson Shimizu
- Department of StatisticsFederal University of Sao CarlosSao PauloBrazil
| | - Rafael Izbicki
- Department of StatisticsFederal University of Sao CarlosSao PauloBrazil
| | | | | | - Lucas N. Paolucci
- Departamento de Biologia GeralUniversidade Federal de ViçosaViçosaBrazil
| | - Yusuf Jameel
- School of Forest, Fisheries, and Geomatics SciencesUniversity of FloridaGainesvilleFloridaUSA
| | - Paulo Brando
- Department of Earth System ScienceUniversity of California, IrvineIrvineCaliforniaUSA
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9
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Li G, Sretenovic S, Eisenstein E, Coleman G, Qi Y. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid. Plant Biotechnol J 2021; 19:1086-1088. [PMID: 33742755 PMCID: PMC8196628 DOI: 10.1111/pbi.13581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Gen Li
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMarylandUSA
| | - Gary Coleman
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
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10
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Mathur S, DeWoody JA. Genetic load has potential in large populations but is realized in small inbred populations. Evol Appl 2021; 14:1540-1557. [PMID: 34178103 PMCID: PMC8210801 DOI: 10.1111/eva.13216] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., adaptive potential) to respond to ecological stressors. We are interested in how the variation captured in protein-coding genes fluctuates relative to overall genomic diversity and whether smaller populations suffer greater costs due to their genetic load of deleterious mutations compared with larger populations. We analyzed individual whole-genome sequences (N = 74) from three different populations of Montezuma quail (Cyrtonyx montezumae), a small ground-dwelling bird that is sustainably harvested in some portions of its range but is of conservation concern elsewhere. Our historical demographic results indicate that Montezuma quail populations in the United States exhibit low levels of genomic diversity due in large part to long-term declines in effective population sizes over nearly a million years. The smaller and more isolated Texas population is significantly more inbred than the large Arizona and the intermediate-sized New Mexico populations we surveyed. The Texas gene pool has a significantly smaller proportion of strongly deleterious variants segregating in the population compared with the larger Arizona gene pool. Our results demonstrate that even in small populations, highly deleterious mutations are effectively purged and/or lost due to drift. However, we find that in small populations the realized genetic load is elevated because of inbreeding coupled with a higher frequency of slightly deleterious mutations that are manifested in homozygotes. Overall, our study illustrates how population genomics can be used to proactively assess both neutral and functional aspects of contemporary genetic diversity in a conservation framework while simultaneously considering deeper demographic histories.
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Affiliation(s)
- Samarth Mathur
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Present address:
Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA
| | - J. Andrew DeWoody
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
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11
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Zhu J, Jeong JS, Khang CH. Tandem DNA repeats contain cis-regulatory sequences that activate biotrophy-specific expression of Magnaporthe effector gene PWL2. Mol Plant Pathol 2021; 22:508-521. [PMID: 33694285 PMCID: PMC8035637 DOI: 10.1111/mpp.13038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
During plant infection, fungi secrete effector proteins in coordination with distinct infection stages. Thus, the success of plant infection is determined by precise control of effector gene expression. We analysed the PWL2 effector gene of the rice blast fungus Magnaporthe oryzae to understand how effector genes are activated specifically during the early biotrophic stages of rice infection. Here, we used confocal live-cell imaging of M. oryzae transformants with various PWL2 promoter fragments fused to sensitive green fluorescent protein reporter genes to determine the expression patterns of PWL2 at the cellular level, together with quantitative reverse transcription PCR analyses at the tissue level. We found PWL2 expression was coupled with sequential biotrophic invasion of rice cells. PWL2 expression was induced in the appressorium upon penetration into a living rice cell but greatly declined in the highly branched hyphae when the first-invaded rice cell was dead. PWL2 expression then increased again as the hyphae penetrate into living adjacent cells. The expression of PWL2 required fungal penetration into living plant cells of either host rice or nonhost onion. Deletion and mutagenesis experiments further revealed that the tandem repeats in the PWL2 promoter contain 12-base pair sequences required for expression. We conclude that PWL2 expression is (a) activated by an unknown signal commonly present in living plant cells, (b) specific to biotrophic stages of fungal infection, and (c) requires 12-base pair cis-regulatory sequences in the promoter.
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Affiliation(s)
- Jie Zhu
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Present address:
Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jun Seop Jeong
- Department of BiologyNorth Carolina A&T State UniversityGreensboroNorth CarolinaUSA
| | - Chang Hyun Khang
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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12
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Huang CY, Niu D, Kund G, Jones M, Albrecht U, Nguyen L, Bui C, Ramadugu C, Bowman KD, Trumble J, Jin H. Identification of citrus immune regulators involved in defence against Huanglongbing using a new functional screening system. Plant Biotechnol J 2021; 19:757-766. [PMID: 33108698 PMCID: PMC8051609 DOI: 10.1111/pbi.13502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/27/2020] [Accepted: 10/18/2020] [Indexed: 05/24/2023]
Abstract
Huanglongbing (HLB) is the most devastating citrus disease in the world. Almost all commercial citrus varieties are susceptible to the causal bacterium, Candidatus Liberibacter asiaticus (CLas), which is transmitted by the Asian citrus psyllid (ACP). Currently, there are no effective management strategies to control HLB. HLB-tolerant traits have been reported in some citrus relatives and citrus hybrids, which offer a direct pathway for discovering natural defence regulators to combat HLB. Through comparative analysis of small RNA profiles and target gene expression between an HLB-tolerant citrus hybrid (Poncirus trifoliata × Citrus reticulata) and a susceptible citrus variety, we identified a panel of candidate defence regulators for HLB-tolerance. These regulators display similar expression patterns in another HLB-tolerant citrus relative, with a distinct genetic and geographic background, the Sydney hybrid (Microcitrus virgata). Because the functional validation of candidate regulators in tree crops is always challenging, we developed a novel rapid functional screening method, using a C. Liberibacter solanacearum (CLso)/potato psyllid/Nicotiana benthamiana interaction system to mimic the natural transmission and infection circuit of the HLB complex. When combined with efficient virus-induced gene silencing in N. benthamiana, this innovative and cost-effective screening method allows for rapid identification and functional characterization of regulators involved in plant immune responses against HLB, such as the positive regulator BRCA1-Associated Protein, and the negative regulator Vascular Associated Death Protein.
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Affiliation(s)
- Chien Yu Huang
- Department of Microbiology and Plant PathologyCenter for Plant Cell BiologyUniversity of CaliforniaRiversideCAUSA
| | - DongDong Niu
- Department of Microbiology and Plant PathologyCenter for Plant Cell BiologyUniversity of CaliforniaRiversideCAUSA
- Department of Plant ProtectionNanjing Agriculture UniversityNanjingChina
| | | | | | - Ute Albrecht
- Horticultural Sciences DepartmentSouthwest Florida Research and Education CenterUniversity of Florida/IFASImmokaleeFLUSA
| | - Lincoln Nguyen
- Department of Microbiology and Plant PathologyCenter for Plant Cell BiologyUniversity of CaliforniaRiversideCAUSA
| | - Christine Bui
- Department of Microbiology and Plant PathologyCenter for Plant Cell BiologyUniversity of CaliforniaRiversideCAUSA
| | | | - Kim D. Bowman
- US Horticultural Research LaboratoryAgricultural Research ServiceUSDAFort PierceFLUSA
| | | | - Hailing Jin
- Department of Microbiology and Plant PathologyCenter for Plant Cell BiologyUniversity of CaliforniaRiversideCAUSA
- Institute for Integrative Genome BiologyUCRCAUSA
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13
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Lin C, Sponsler DB, Richardson RT, Watters HD, Glinski DA, Henderson WM, Minucci JM, Lee EH, Purucker ST, Johnson RM. Honey Bees and Neonicotinoid-Treated Corn Seed: Contamination, Exposure, and Effects. Environ Toxicol Chem 2021; 40:1212-1221. [PMID: 33289922 PMCID: PMC8048971 DOI: 10.1002/etc.4957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/09/2020] [Accepted: 12/01/2020] [Indexed: 05/05/2023]
Abstract
Most corn (Zea mays) seeds planted in the United States in recent years are coated with a seed treatment containing neonicotinoid insecticides. Abrasion of the seed coating generates insecticide-laden planter dust that disperses through the landscape during corn planting and has resulted in many "bee-kill" incidents in North America and Europe. We investigated the linkage between corn planting and honey bee colony success in a region dominated by corn agriculture. Over 3 yr we consistently observed an increased presence of corn seed treatment insecticides in bee-collected pollen and elevated worker bee mortality during corn planting. Residues of seed treatment neonicotinoids, clothianidin and thiamethoxam, detected in pollen positively correlated with cornfield area surrounding the apiaries. Elevated worker mortality was also observed in experimental colonies fed field-collected pollen containing known concentrations of corn seed treatment insecticides. We monitored colony growth throughout the subsequent year in 2015 and found that colonies exposed to higher insecticide concentrations exhibited slower population growth during the month of corn planting but demonstrated more rapid growth in the month following, though this difference may be related to forage availability. Exposure to seed treatment neonicotinoids during corn planting has clear short-term detrimental effects on honey bee colonies and may affect the viability of beekeeping operations that are dependent on maximizing colony size in the springtime. Environ Toxicol Chem 2021;40:1212-1221. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Chia‐Hua Lin
- Department of Entomology, Ohio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOhioUSA
| | - Douglas B. Sponsler
- Department of Entomology, Ohio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOhioUSA
| | - Rodney T. Richardson
- Department of Entomology, Ohio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOhioUSA
| | - Harold D. Watters
- Department of ExtensionThe Ohio State UniversityBellefontaineOhioUSA
| | | | - W. Matthew Henderson
- Center for Environmental Measurement and ModelingUS Environmental Protection AgencyAthensGeorgia
| | - Jeffrey M. Minucci
- Center for Computational Toxicity and ExposureUS Environmental Protection Agency, Research Triangle ParkNorth Carolina
| | - E. Henry Lee
- Center for Public Health and Environmental AssessmentUS Environmental Protection AgencyCorvallisOregon
| | - S. Thomas Purucker
- Center for Computational Toxicity and ExposureUS Environmental Protection Agency, Research Triangle ParkNorth Carolina
| | - Reed M. Johnson
- Department of Entomology, Ohio Agricultural Research and Development CenterThe Ohio State UniversityWoosterOhioUSA
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14
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Strickland BK, Brooke JM, Zischke MT, Lashley MA. Podcasting as a tool to take conservation education online. Ecol Evol 2021; 11:3597-3606. [PMID: 33898012 PMCID: PMC8057326 DOI: 10.1002/ece3.7353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Traditional forms of higher learning include teaching in the classroom on college campuses and in-person adult-focused public outreach events for non-students. Online college degree programs and public outreach platforms have been steadily emerging, and the COVID-19 pandemic has, at least temporarily, forced all related ecology and evolutionary biology programs to move to online delivery. Podcasting is a form of online mass communication that is rapidly gaining popularity and has the flexibility to be incorporated into the pedagogical toolbox for the online classroom and remote public outreach programming. Podcasting is also becoming more popular in the ecology and evolutionary biology field. Here, we describe the great potential of podcasting to transform the learning experience, present a case study of success from the United States, provide a table of podcast recommended by ecologist responding to a listserv, and provide a road map for adoption and utilization of podcasting for the future.
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Affiliation(s)
- Bronson K. Strickland
- Department of Wildlife, Fisheries, and AquacultureMississippi State UniversityMississippi StateMSUSA
| | - Jarred M. Brooke
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
| | - Mitchell T. Zischke
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
| | - Marcus A. Lashley
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFLUSA
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15
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Ngaki MN, Sahoo DK, Wang B, Bhattacharyya MK. Overexpression of a plasma membrane protein generated broad-spectrum immunity in soybean. Plant Biotechnol J 2021; 19:502-516. [PMID: 32954627 PMCID: PMC7957895 DOI: 10.1111/pbi.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/17/2020] [Accepted: 08/06/2020] [Indexed: 05/10/2023]
Abstract
Plants fight-off pathogens and pests by manifesting an array of defence responses using their innate immunity mechanisms. Here we report the identification of a novel soybean gene encoding a plasma membrane protein, transcription of which is suppressed following infection with the fungal pathogen, Fusarium virguliforme. Overexpression of the protein led to enhanced resistance against not only against F. virguliforme, but also against spider mites (Tetranychus urticae, Koch), soybean aphids (Aphis glycines, Matsumura) and soybean cyst nematode (Heterodera glycines). We, therefore, name this protein as Glycine max disease resistance 1 (GmDR1; Glyma.10g094800). The homologues of GmDR1 have been detected only in legumes, cocoa, jute and cotton. The deduced GmDR1 protein contains 73 amino acids. GmDR1 is predicted to contain an ecto- and two transmembrane domains. Transient expression of the green fluorescent protein fused GmDR1 protein in soybean leaves showed that it is a plasma membrane protein. We investigated if chitin, a pathogen-associated molecular pattern (PAMP), common to all pathogen and pests considered in this study, can significantly enhance defence pathways among the GmDR1-overexpressed transgenic soybean lines. Chitin induces marker genes of the salicylic- and jasmonic acid-mediated defence pathways, but suppresses the defence pathway regulated by ethylene. Chitin induced SA- and JA-regulated defence pathways may be one of the mechanisms involved in generating broad-spectrum resistance among the GmDR1-overexpressed transgenic soybean lines against two serious pathogens and two pests including spider mites, against which no known resistance genes have been identified in soybean and among the most other crop species.
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Affiliation(s)
| | | | - Bing Wang
- Department of AgronomyIowa State UniversityAmesIAUSA
- Present address:
Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
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16
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Crow TM, Buerkle CA, Runcie DE, Hufford KM. Implications of genetic heterogeneity for plant translocation during ecological restoration. Ecol Evol 2021; 11:1100-1110. [PMID: 33598117 PMCID: PMC7863393 DOI: 10.1002/ece3.6978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/23/2022] Open
Abstract
Ecological restoration often requires translocating plant material from distant sites. Importing suitable plant material is important for successful establishment and persistence. Yet, published guidelines for seed transfer are available for very few species. Accurately predicting how transferred plants will perform requires multiyear and multi-environment field trials and comprehensive follow-up work, and is therefore infeasible given the number of species used in restoration programs. Alternative methods to predict the outcomes of seed transfer are valuable for species without published guidelines. In this study, we analyzed the genetic structure of an important shrub used in ecological restoration in the Southern Rocky Mountains called alder-leaf mountain mahogany (Cercocarpus montanus). We sequenced DNA from 1,440 plants in 48 populations across a broad geographic range. We found that genetic heterogeneity among populations reflected the complex climate and topography across which the species is distributed. We identified temperature and precipitation variables that were useful predictors of genetic differentiation and can be used to generate seed transfer recommendations. These results will be valuable for defining management and restoration practices for mountain mahogany.
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Affiliation(s)
- Taylor M. Crow
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
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17
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Dean AN, Niemi JB, Tyndall JC, Hodgson EW, O'Neal ME. Developing a decision-making framework for insect pest management: a case study using Aphis glycines (Hemiptera: Aphididae). Pest Manag Sci 2021; 77:886-894. [PMID: 32949094 PMCID: PMC7821323 DOI: 10.1002/ps.6093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/20/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The profitability of farming varies based on factors such as a crop's market value, input costs and occurrence of resistant pests, all capable of altering the value of pest management tactics in an integrated pest management program. We provide a framework for calculating expected yield and expected net revenue of pest management scenarios, using the soybean aphid (Aphis glycines) as a case study. Foliar insecticide and host-plant resistance are effective management tactics for preventing yield loss from soybean aphid outbreaks; however, pyrethroid-resistant aphid populations pose a management challenge for farmers. We evaluated eight scenarios relevant to soybean aphid management in Iowa with varying probabilities of aphid outbreaks and insecticide-resistant aphids occurring. RESULTS Our equation suggests that insecticide use is profitable when the probability of an aphid outbreak is ≥29%, and soybean production will become more costly with increasing probability of pyrethroid-resistant aphids. If farmers continue to use pyrethroids, they will not experience financial consequences from pyrethroid-resistant aphids until the chance of insecticide resistance is 48%. Aphid-resistant varieties provided consistent yield and offered the highest net revenue under all conditions. CONCLUSION This framework can be used for other crop-pest systems to evaluate the profitability of management tactics and investigate how resistance impacts revenue for farmers. Including the cost of resistance in crop budgets can help farmers and agronomic consultants comprehend these impacts and enhance decision-making to increase revenue and curb resistance development.
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Affiliation(s)
- Ashley N Dean
- Department of EntomologyIowa State UniversityAmesIAUSA
| | - Jarad B Niemi
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - John C Tyndall
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmesIAUSA
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18
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López‐Martínez G, Carpenter JE, Hight SD, Hahn DA. Low-oxygen hormetic conditioning improves field performance of sterile insects by inducing beneficial plasticity. Evol Appl 2021; 14:566-576. [PMID: 33664795 PMCID: PMC7896707 DOI: 10.1111/eva.13141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/29/2022] Open
Abstract
As part of sterile insect technique (SIT) programs, irradiation can effectively induce sterility in insects by damaging germline genomic DNA. However, irradiation also induces other off-target side effects that reduce the quality and performance of sterilized males, including the formation of damaging free radicals that can reduce sterile male performance. Thus, treatments that reduce off-target effects of irradiation on male performance while maintaining sterility can improve the feasibility and economy of SIT programs. We previously found that inducing a form of rapid, beneficial plasticity with a 1-hr anoxic-conditioning period (physiological conditioning hormesis) prior to and during irradiation improves male field performance in the laboratory while maintaining sterility in males of the cactus moth, Cactoblastis cactorum. Here, we extend this work by testing the extent to which this beneficial plasticity may improve male field performance and longevity in the field. Based on capture rates after a series of mark release-recapture experiments, we found that anoxia-conditioned irradiated moths were active in the field longer than their irradiated counterparts. In addition, anoxia-conditioned moths were captured in traps that were farther away from the release site than unconditioned moths, suggesting greater dispersal. These data confirmed that beneficial plasticity induced by anoxia hormesis prior to irradiation led to lower postirradiation damage and increased flight performance and recapture duration under field conditions. We recommend greater consideration of beneficial plasticity responses in biological control programs and specifically the implementation of anoxia-conditioning treatments applied prior to irradiation in area-wide integrated pest management programs that use SIT.
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Affiliation(s)
- Giancarlo López‐Martínez
- Department of Entomology and NematologyUniversity of FloridaGainesvilleFloridaUSA
- Department of Biological SciencesNorth Dakota State UniversityFargoNorth DakotaUSA
| | | | - Stephen D. Hight
- USDA‐ARS Center for Medical, Agricultural, & Veterinary EntomologyTallahasseeFloridaUSA
| | - Daniel A. Hahn
- Department of Entomology and NematologyUniversity of FloridaGainesvilleFloridaUSA
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19
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Chen X, Liu B, Li X, An TT, Zhou Y, Li G, Wu‐Smart J, Alvarez S, Naldrett MJ, Eudy J, Kubik G, Wilson RA, Kachman SD, Cui J, Yu J. Identification of anti-inflammatory vesicle-like nanoparticles in honey. J Extracell Vesicles 2021; 10:e12069. [PMID: 33613874 PMCID: PMC7879699 DOI: 10.1002/jev2.12069] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 01/05/2021] [Accepted: 01/31/2021] [Indexed: 12/11/2022] Open
Abstract
Honey has been used as a nutrient, an ointment, and a medicine worldwide for many centuries. Modern research has demonstrated that honey has many medicinal properties, reflected in its anti-microbial, anti-oxidant, and anti-inflammatory bioactivities. Honey is composed of sugars, water and a myriad of minor components, including minerals, vitamins, proteins and polyphenols. Here, we report a new bioactive component‒vesicle-like nanoparticles‒in honey (H-VLNs). These H-VLNs are membrane-bound nano-scale particles that contain lipids, proteins and small-sized RNAs. The presence of plant-originated plasma transmembrane proteins and plasma membrane-associated proteins suggests the potential vesicle-like nature of these particles. H-VLNs impede the formation and activation of the nucleotide-binding domain and leucine-rich repeat related (NLR) family, pyrin domain containing 3 (NLRP3) inflammasome, which is a crucial inflammatory signalling platform in the innate immune system. Intraperitoneal administration of H-VLNs in mice alleviates inflammation and liver damage in the experimentally induced acute liver injury. miR-4057 in H-VLNs was identified in inhibiting NLRP3 inflammasome activation. Together, our studies have identified anti-inflammatory VLNs as a new bioactive agent in honey.
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Affiliation(s)
- Xingyi Chen
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Baolong Liu
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Xingzhi Li
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Thuy T. An
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - You Zhou
- Center for BiotechnologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Gang Li
- Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Judy Wu‐Smart
- Department of EntomologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Sophie Alvarez
- Nebraska Center for Biotechnology, University of Nebraska‐LincolnProteomics and Metabolomics FacilityNebraskaUSA
| | - Michael J. Naldrett
- Nebraska Center for Biotechnology, University of Nebraska‐LincolnProteomics and Metabolomics FacilityNebraskaUSA
| | - James Eudy
- Department of Genetics Cell Biology and AnatomyUniversity of Nebraska Medical Center, 985915 Nebraska Medical CenterOmahaNebraskaUSA
| | - Gregory Kubik
- Genomics Core Facility, University of Nebraska Medical CenterOmahaNebraskaUSA
| | - Richard A. Wilson
- Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Stephen D. Kachman
- Department of StatisticsUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Juan Cui
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Jiujiu Yu
- Department of Nutrition and Health SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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20
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Peng J, Schachterle JK, Sundin GW. Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of the Hfq-dependent small RNA RprA. Mol Plant Pathol 2021; 22:255-270. [PMID: 33314618 PMCID: PMC7814967 DOI: 10.1111/mpp.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting symptoms. Although E. amylovora is well known to be able to cause systemic infection, how biofilm cells of E. amylovora transit from the sessile mode of growth in xylem to the planktonic mode of growth in cortical parenchyma remains unknown. Increasing evidence has suggested the important modulatory roles of Hfq-dependent small RNAs (sRNAs) in the pathogenesis of E. amylovora. Here, we demonstrate that the sRNA RprA acts as a positive regulator of amylovoran exopolysaccharide production, the type III secretion system (T3SS), and flagellar-dependent motility, and as a negative regulator of levansucrase activity and cellulose production. We also show that RprA affects the promoter activity of multiple virulence factor genes and regulates hrpS, a critical T3SS regulator, at the posttranscriptional level. We determined that rprA expression can be activated by the Rcs phosphorelay, and that expression is active during T3SS-mediated host infection in an immature pear fruit infection model. We further showed that overexpression of rprA activated the in vitro dispersal of E. amylovora cells from biofilms. Thus, our investigation of the varied role of RprA in affecting E. amylovora virulence provides important insights into the functions of this sRNA in biofilm control and systemic infection.
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Affiliation(s)
- Jingyu Peng
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Jeffrey K. Schachterle
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
- Present address:
US National Arboretum – Floral and Nursery Plants Research UnitUSDA‐ARSBeltsvilleMarylandUSA
| | - George W. Sundin
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
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21
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Herzog SA, Latvis M. Examining the utility of DNA barcodes for the identification of tallgrass prairie flora. Appl Plant Sci 2021; 9:e11405. [PMID: 33552747 PMCID: PMC7845766 DOI: 10.1002/aps3.11405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The tallgrass prairies of North America are one of the most threatened ecosystems in the world, making efficient species identification essential for understanding and managing diversity. Here, we assess DNA barcoding with high-throughput sequencing as a method for rapid plant species identification. METHODS Using herbarium collections representing the tallgrass prairie flora of Oak Lake Field Station, South Dakota, USA, we amplified and examined four common nuclear and plastid barcode regions (ITS, matK, psbA-trnH, and rbcL), individually and in combination, to test their success in identifying samples to family, genus, and species levels using BLAST searches of three databases of varying size. RESULTS Concatenated barcodes increased performance, although none were significantly different than single-region barcodes. The plastid region psbA-trnH performed significantly more poorly than the others, while barcodes containing ITS performed best. Database size significantly affected identification success at all three taxonomic levels. Confident species-level identification ranged from 8-44% for the global database, 13-56% for the regional database, and 21-80% for the sampled species database, depending on the barcode used. DISCUSSION Barcoding was generally successful in identifying tallgrass prairie genera and families, but was of limited use in species-level identifications. Database size was an important factor in successful plant identification. We discuss future directions and considerations for improving the performance of DNA barcoding in tallgrass prairies.
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Affiliation(s)
- Sarah A. Herzog
- Department of Natural Resource ManagementSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
- C. A. Taylor HerbariumSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
| | - Maribeth Latvis
- Department of Natural Resource ManagementSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
- C. A. Taylor HerbariumSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
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22
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Huerta AI, Delorean EE, Bossa‐Castro AM, Tonnessen BW, Raghavan C, Corral R, Pérez‐Quintero ÁL, Leung H, Verdier V, Leach JE. Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae. Plant Biotechnol J 2021; 19:51-63. [PMID: 32594636 PMCID: PMC7769240 DOI: 10.1111/pbi.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 05/07/2023]
Abstract
Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.
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Affiliation(s)
- Alejandra I. Huerta
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Emily E. Delorean
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ana M. Bossa‐Castro
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Bradley W. Tonnessen
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Extension Plant SciencesNew Mexico State UniversityLas CrucesNM88003USA
| | - Chitra Raghavan
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Queensland Department of Agriculture and FisheriesHorticulture and Forestry SciencesCairnsQLD4870Australia
| | - Rene Corral
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | | | - Hei Leung
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
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Akbari A, Wang Z, He P, Wang D, Lee J, Han IL, Li G, Gu AZ. Unrevealed roles of polyphosphate-accumulating microorganisms. Microb Biotechnol 2021; 14:82-87. [PMID: 33404187 PMCID: PMC7888455 DOI: 10.1111/1751-7915.13730] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/29/2022] Open
Abstract
We first review current knowledge on PAOs, with a focus on bacteria, in terms of their phylogenetic identities, metabolic pathways and detection methods. We further discuss the evidence that suggests the ubiquitous presence of PAOs in nature and point out the unrevealed roles of the PAOs that warrant future investigation.
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Affiliation(s)
- Ali Akbari
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - ZiJian Wang
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Peisheng He
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Dongqi Wang
- State Key Laboratory of Eco‐hydraulics in Northwest Arid RegionXi’an University of TechnologyXi’anShaanxi710048China
| | - Jangho Lee
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - IL Han
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Guangyu Li
- Department of Civil and Environmental EngineeringNortheastern University360 Huntington AvenueBostonMA02115USA
| | - April Z. Gu
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
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24
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Chen AYS, Peng JHC, Polek M, Tian T, Ludman M, Fátyol K, Ng JCK. Comparative analysis identifies amino acids critical for citrus tristeza virus (T36CA) encoded proteins involved in suppression of RNA silencing and differential systemic infection in two plant species. Mol Plant Pathol 2021; 22:64-76. [PMID: 33118689 PMCID: PMC7749750 DOI: 10.1111/mpp.13008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
Complementary (c)DNA clones corresponding to the full-length genome of T36CA (a Californian isolate of Citrus tristeza virus with the T36 genotype), which shares 99.1% identity with that of T36FL (a T36 isolate from Florida), were made into a vector system to express the green fluorescent protein (GFP). Agroinfiltration of two prototype T36CA-based vectors (pT36CA) to Nicotiana benthamiana plants resulted in local but not systemic GFP expression/viral infection. This contrasted with agroinfiltration of the T36FL-based vector (pT36FL), which resulted in both local and systemic GFP expression/viral infection. A prototype T36CA systemically infected RNA silencing-defective N. benthamiana lines, demonstrating that a genetic basis for its defective systemic infection was RNA silencing. We evaluated the in planta bioactivity of chimeric pT36CA-pT36FL constructs and the results suggested that nucleotide variants in several open reading frames of the prototype T36CA could be responsible for its defective systemic infection. A single amino acid substitution in each of two silencing suppressors, p20 (S107G) and p25 (G36D), of prototype T36CA facilitated its systemic infectivity in N. benthamiana (albeit with reduced titre relative to that of T36FL) but not in Citrus macrophylla plants. Enhanced virus accumulation and, remarkably, robust systemic infection of T36CA in N. benthamiana and C. macrophylla plants, respectively, required two additional amino acid substitutions engineered in p65 (N118S and S158L), a putative closterovirus movement protein. The availability of pT36CA provides a unique opportunity for comparative analysis to identify viral coding and noncoding nucleotides or sequences involved in functions that are vital for in planta infection.
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Affiliation(s)
- Angel Y. S. Chen
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - James H. C. Peng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - MaryLou Polek
- National Clonal Germplasm Repository for Citrus & DatesUSDA ARSRiversideCaliforniaUSA
| | - Tongyan Tian
- California Department of Food and AgricultureSacramentoCaliforniaUSA
| | - Márta Ludman
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - Károly Fátyol
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - James C. K. Ng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
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25
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Leon RG, Dunne JC, Gould F. The role of population and quantitative genetics and modern sequencing technologies to understand evolved herbicide resistance and weed fitness. Pest Manag Sci 2021; 77:12-21. [PMID: 32633005 PMCID: PMC7754128 DOI: 10.1002/ps.5988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 05/11/2023]
Abstract
Evolution of resistance to multiple herbicides with different sites of action and of nontarget site resistance (NTSR) often involves multiple genes. Thus, single-gene analyses, typical in studies of target site resistance, are not sufficient for understanding the genetic architecture and dynamics of NTSR and multiple resistance. The genetics of weed adaptation to varied agricultural environments is also generally expected to be polygenic. Recent advances in whole-genome sequencing as well as bioinformatic and statistical tools have made it possible to use population and quantitative genetics methods to expand our understanding of how resistance and other traits important for weed adaptation are genetically controlled at the individual and population levels, and to predict responses to selection pressure by herbicides and other environmental factors. The use of tools such as quantitative trait loci mapping, genome-wide association studies, and genomic prediction will allow pest management scientists to better explain how pests adapt to control tools and how specific genotypes thrive and spread across agroecosystems and other human-disturbed systems. The challenge will be to use this knowledge in developing integrated weed management systems that inhibit broad resistance to current and future weed-control methods. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ramon G Leon
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Jeffrey C Dunne
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
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26
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Haase CG, Fuller NW, Dzal YA, Hranac CR, Hayman DTS, Lausen CL, Silas KA, Olson SH, Plowright RK. Body mass and hibernation microclimate may predict bat susceptibility to white-nose syndrome. Ecol Evol 2021; 11:506-515. [PMID: 33437446 PMCID: PMC7790633 DOI: 10.1002/ece3.7070] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
In multihost disease systems, differences in mortality between species may reflect variation in host physiology, morphology, and behavior. In systems where the pathogen can persist in the environment, microclimate conditions, and the adaptation of the host to these conditions, may also impact mortality. White-nose syndrome (WNS) is an emerging disease of hibernating bats caused by an environmentally persistent fungus, Pseudogymnoascus destructans. We assessed the effects of body mass, torpid metabolic rate, evaporative water loss, and hibernaculum temperature and water vapor deficit on predicted overwinter survival of bats infected by P. destructans. We used a hibernation energetics model in an individual-based model framework to predict the probability of survival of nine bat species at eight sampling sites across North America. The model predicts time until fat exhaustion as a function of species-specific host characteristics, hibernaculum microclimate, and fungal growth. We fit a linear model to determine relationships with each variable and predicted survival and semipartial correlation coefficients to determine the major drivers in variation in bat survival. We found host body mass and hibernaculum water vapor deficit explained over half of the variation in survival with WNS across species. As previous work on the interplay between host and pathogen physiology and the environment has focused on species with narrow microclimate preferences, our view on this relationship is limited. Our results highlight some key predictors of interspecific survival among western bat species and provide a framework to assess impacts of WNS as the fungus continues to spread into western North America.
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Affiliation(s)
- Catherine G. Haase
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
- Present address:
Department of BiologyAustin Peay State UniversityClarksvilleTNUSA
| | - Nathan W. Fuller
- Department of Biological SciencesTexas Tech UniversityLubbockTXUSA
- Present address:
Texas Parks and Wildlife DepartmentNongame and Rare Species ProgramAustinTXUSA
| | - Yvonne A. Dzal
- Department of BiologyCentre for Forest Interdisciplinary Research (C‐FIR)University of WinnipegWinnipegMBCanada
| | - C. Reed Hranac
- Molecular Epidemiology and Public Health LaboratoryMassey UniversityPalmerston NorthNew Zealand
| | - David T. S. Hayman
- Molecular Epidemiology and Public Health LaboratoryMassey UniversityPalmerston NorthNew Zealand
| | | | | | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
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27
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Fu Z, Meier AR, Epstein B, Bergland AO, Castillo Carrillo CI, Cooper WR, Cruzado RK, Horton DR, Jensen AS, Kelley JL, Rashed A, Reitz SR, Rondon SI, Thinakaran J, Wenninger EJ, Wohleb CH, Crowder DW, Snyder WE. Host plants and Wolbachia shape the population genetics of sympatric herbivore populations. Evol Appl 2020; 13:2740-2753. [PMID: 33294020 PMCID: PMC7691456 DOI: 10.1111/eva.13079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 01/06/2023] Open
Abstract
Changing climate and land-use practices have the potential to bring previously isolated populations of pest insects into new sympatry. This heightens the need to better understand how differing patterns of host-plant association, and unique endosymbionts, serve to promote genetic isolation or integration. We addressed these factors in populations of potato psyllid, Bactericera cockerelli (Šulc), a generalist herbivore that vectors a bacterial pathogen (Candidatus Liberibacter solanacearum, causal pathogen of zebra chip disease) of potato (Solanum tuberosum L.). Genome-wide SNP data revealed two major genetic clusters-psyllids collected from potato crops were genetically similar to psyllids found on a common weed, Lycium spp., but dissimilar from those found on another common non-crop host, Solanum dulcamara L. Most psyllids found on Lycium spp. and potato represented a single mitochondrial cytochrome oxidase I (COI) haplotype that has been suggested to not be native to the region, and whose arrival may have been concurrent with zebra chip disease first emerging. The putatively introduced COI haplotype usually co-occurred with endosymbiotic Wolbachia, while the putatively resident COI haplotype generally did not. Genetic intermediates between the two genetic populations of insects were rare, consistent with recent sympatry or reproductive isolation, although admixture patterns of apparent hybrids were consistent with introgression of genes from introduced into resident populations. Our results suggest that both host-plant associations and endosymbionts are shaping the population genetic structure of sympatric psyllid populations associated with different non-crop hosts. It is of future interest to explicitly examine vectorial capacity of the two populations and their potential hybrids, as population structure and hybridization might alter regional vector capacity and disease outbreaks.
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Affiliation(s)
- Zhen Fu
- Department of EntomologyWashington State UniversityPullmanWAUSA
- Present address:
Department of EntomologyTexas A&M UniversityCollege StationTXUSA
| | | | - Brendan Epstein
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMNUSA
| | | | - Carmen I. Castillo Carrillo
- Departamento de Protección VegetalEstación Experimental Santa CatalinaInstituto Nacional de Investigaciones Agropecuarias (INIAP)QuitoEcuador
| | | | - Regina K. Cruzado
- Department of Entomology, Plant Pathology, and NematologyUniversity of IdahoMoscowIDUSA
| | - David R. Horton
- Temperate Tree Fruit and Vegetable ResearchUSDA‐ARSWapatoWAUSA
| | | | - Joanna L. Kelley
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | - Arash Rashed
- Department of Entomology, Plant Pathology, and NematologyUniversity of IdahoMoscowIDUSA
| | - Stuart R. Reitz
- Malheur Experiment StationOregon State UniversityOntarioORUSA
| | - Silvia I. Rondon
- Department of Crop and Soil ScienceHermiston Agricultural Research and Extension CenterHermistonORUSA
| | | | - Erik J. Wenninger
- Department of Entomology, Plant Pathology, and NematologyKimberly Research and Extension CenterUniversity of IdahoKimberlyIDUSA
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28
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Johnson KM. As Births Diminish and Deaths Increase, Natural Decrease becomes More Widespread in Rural America. Rural Sociol 2020; 85:1045-1058. [PMID: 33362301 PMCID: PMC7753390 DOI: 10.1111/ruso.12358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 05/30/2023]
Abstract
Even before the onset of the Covid-19 pandemic, the U.S. population growth rate last year was the lowest in 100 years. And, from 2010 to 2019 nonmetropolitan America lost population for the first time in history. Diminished natural increase was a major contributor to this and also accelerated the incidence of natural decrease (more deaths than births), particularly in rural America. Deaths exceeded births in 46 percent of all U.S. counties-a near record high. Nearly 79 percent of these natural decrease counties were nonmetropolitan. This research uses recent data and a multivariate spatial regression model to update our understanding of the growing incidence of natural decrease in both rural and urban America. In light of the mortality increase and likely fertility declines stemming from the Covid-19 pandemic, these findings have significant implications for future nonmetropolitan demographic trends.
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Affiliation(s)
- Kenneth M. Johnson
- Department of Sociology and Carsey School of Public PolicyUniversity of New Hampshire
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29
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Perfecto I, Vandermeer J. The assembly and importance of a novel ecosystem: The ant community of coffee farms in Puerto Rico. Ecol Evol 2020; 10:12650-12662. [PMID: 33304482 PMCID: PMC7713940 DOI: 10.1002/ece3.6785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/13/2020] [Accepted: 08/13/2020] [Indexed: 11/18/2022] Open
Abstract
Agricultural ecosystems are by their very nature novel and by definition the more general biodiversity associated with them must likewise constitute a novel community. Here, we examine the community of arboreally foraging ants in the coffee agroecosystem of Puerto Rico. We surveyed 20 coffee plants in 25 farms three times in a period of one year. We also conducted a more spatially explicit sampling in two of the farms and conducted a species interaction study between the two most abundant species, Wasmannia auropunctata and Solenopsis invicta, in the laboratory. We find that the majority of the most common species are well-known invasive ants and that there is a highly variable pattern of dominance that varies considerably over the main coffee producing region of Puerto Rico, suggesting an unusual modality of community structure. The distribution pattern of the two most common species, W. auropunctata and S. invicta, suggests strong competitive exclusion. However, they also have opposite relationships with the percent of shade cover, with W. auropunctata showing a positive relationship with shade, while S. invicta has a negative relationship. The spatial distribution of these two dominant species in the two more intensively studied farms suggests that young colonies of S. invicta can displace W. auropunctata. Laboratory experiments confirm this. In addition to the elaboration of the nature and extent of this novel ant community, we speculate on the possibilities of its active inclusion as part of a biological control system dealing with several coffee pests, including one of the ants itself, W. auropunctata.
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Affiliation(s)
- Ivette Perfecto
- School for Environment and SustainabilityUniversity of MichiganAnn ArborMIUSA
| | - John Vandermeer
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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30
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Jia Z, Yue F, Chen X, Narayanan N, Qiu J, Syed SA, Imbalzano AN, Deng M, Yu P, Hu C, Kuang S. Protein Arginine Methyltransferase PRMT5 Regulates Fatty Acid Metabolism and Lipid Droplet Biogenesis in White Adipose Tissues. Adv Sci (Weinh) 2020; 7:2002602. [PMID: 33304767 PMCID: PMC7709973 DOI: 10.1002/advs.202002602] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 02/06/2023]
Abstract
The protein arginine methyltransferase 5 (PRMT5) is an emerging regulator of cancer and stem cells including adipogenic progenitors. Here, a new physiological role of PRMT5 in adipocytes and systemic metabolism is reported. Conditional knockout mice were generated to ablate the Prmt5 gene specifically in adipocytes (Prmt5AKO). The Prmt5AKO mice exhibit sex- and depot-dependent progressive lipodystrophy that is more pronounced in females and in visceral (than subcutaneous) white fat. The lipodystrophy and associated energy imbalance, hyperlipidemia, hepatic steatosis, glucose intolerance, and insulin resistance are exacerbated by high-fat-diet. Mechanistically, Prmt5 methylates and releases the transcription elongation factor SPT5 from Berardinelli-Seip congenital lipodystrophy 2 (Bscl2, encoding Seipin) promoter, and Prmt5AKO disrupts Seipin-mediated lipid droplet biogenesis. Prmt5 also methylates Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a) and promotes lipogenic gene expression, and Prmt5AKO suppresses SREBP1a-dependent fatty acid metabolic pathways in adipocytes. Thus, PRMT5 plays a critical role in regulating lipid metabolism and lipid droplet biogenesis in adipocytes.
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Affiliation(s)
- Zhihao Jia
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Feng Yue
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Xiyue Chen
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Naagarajan Narayanan
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Jiamin Qiu
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMA01605USA
| | - Meng Deng
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIN47907USA
- Bindley Bioscience CenterPurdue UniversityWest LafayetteIN47907USA
| | - Peng Yu
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
- Medical Big Data CenterSichuan UniversityChengdu610041China
| | - Changdeng Hu
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
| | - Shihuan Kuang
- Department of Animal SciencesPurdue UniversityWest LafayetteIN47907USA
- Purdue University Center for Cancer ResearchWest LafayetteIndiana47907USA
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Culshaw‐Maurer M, Sih A, Rosenheim JA. Bugs scaring bugs: enemy-risk effects in biological control systems. Ecol Lett 2020; 23:1693-1714. [PMID: 32902103 PMCID: PMC7692946 DOI: 10.1111/ele.13601] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 08/13/2020] [Indexed: 01/09/2023]
Abstract
Enemy-risk effects, often referred to as non-consumptive effects (NCEs), are an important feature of predator-prey ecology, but their significance has had little impact on the conceptual underpinning or practice of biological control. We provide an overview of enemy-risk effects in predator-prey interactions, discuss ways in which risk effects may impact biocontrol programs and suggest avenues for further integration of natural enemy ecology and integrated pest management. Enemy-risk effects can have important influences on different stages of biological control programs, including natural enemy selection, efficacy testing and quantification of non-target impacts. Enemy-risk effects can also shape the interactions of biological control with other pest management practices. Biocontrol systems also provide community ecologists with some of the richest examples of behaviourally mediated trophic cascades and demonstrations of how enemy-risk effects play out among species with no shared evolutionary history, important topics for invasion biology and conservation. We conclude that the longstanding use of ecological theory by biocontrol practitioners should be expanded to incorporate enemy-risk effects, and that community ecologists will find many opportunities to study enemy-risk effects in biocontrol settings.
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Affiliation(s)
- Michael Culshaw‐Maurer
- Department of Entomology and NematologyUniversity of CaliforniaDavisCA95616USA
- Department of Evolution and EcologyUniversity of CaliforniaDavisCA95616USA
| | - Andrew Sih
- Department of Environmental Science and PolicyUniversity of CaliforniaDavisCA95616USA
| | - Jay A. Rosenheim
- Department of Entomology and NematologyUniversity of CaliforniaDavisCA95616USA
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Acevedo MA. Teaching quantitative ecology online: An evidence-based prescription of best practices. Ecol Evol 2020; 10:12457-12464. [PMID: 33250986 PMCID: PMC7679551 DOI: 10.1002/ece3.6607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022] Open
Abstract
Quantitative skills are becoming central to the undergraduate and graduate curriculum in ecology and evolutionary biology. While previous studies acknowledge that students perceive their quantitative training to be inadequate, there is little guidance on best practices. Moreover, with the recent COVID-19 sudden transition to online learning, there is even less guidance on how to effectively teach quantitative ecology online. Here, I synthesize a prescription of pedagogical best practices for teaching quantitative ecology online based on a broad review of the literature on multiple quantitative disciplines. These best practices include the following: (1) design and implement the class to meet learning goals using online strategies specifically; (2) create an open, inclusive, and welcoming online environment that promotes a sense of learning community; (3) acknowledge the diversity of talents and learning strategies; (4) use real-world examples and assessments; (5) account for gaps in knowledge; (6) emphasize the modeling cycle process; (7) focus on developing ideas rather than tools or procedures; (8) if needed, introduce computational tools thoroughly before combining them with mathematical or statistical concepts; (9) evaluate the course constantly; and (10) put your heart and soul into the class. I hope these practices help fellow instructors of quantitative ecology facing similar challenges in providing our students with the knowledge and skills needed to meet the challenges of the future.
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Affiliation(s)
- Miguel A. Acevedo
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFloridaUSA
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33
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Jia H, Wang N. Generation of homozygous canker-resistant citrus in the T0 generation using CRISPR-SpCas9p. Plant Biotechnol J 2020; 18:1990-1992. [PMID: 32167662 PMCID: PMC7540605 DOI: 10.1111/pbi.13375] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 05/09/2023]
Affiliation(s)
- Hongge Jia
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFlUSA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceInstitute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFlUSA
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Kaplan I, Bokulich NA, Caporaso JG, Enders LS, Ghanem W, Ingerslew KS. Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evol Appl 2020; 13:1984-1999. [PMID: 32908599 PMCID: PMC7463318 DOI: 10.1111/eva.12956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/17/2022] Open
Abstract
Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on-farm "rule of thumb" has never been rigorously tested in a scientific framework. To experimentally evaluate the relationship between phylogenetic distance and crop performance, we used a plant-soil feedback approach whereby 35 crops and weeds varying in their relatedness to tomato (Solanum lycopersicum) were tested in a two-year field experiment. We used community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth. Overall, tomato yield was ca. 15% lower in soil previously cultivated with tomato; yet, past the species level there was no effect of phylogenetic distance on crop performance. Soil microbial communities, on the other hand, were compositionally more similar between close plant relatives. Random forest regression predicted log10 phylogenetic distance to tomato with moderate accuracy (R 2 = .52), primarily driven by bacteria in the genus Sphingobium. These data indicate that, beyond avoiding conspecifics, evolutionary history contributes little to understanding plant-soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness.
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Affiliation(s)
- Ian Kaplan
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
| | - Nicholas A. Bokulich
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | - J. Gregory Caporaso
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | | | - Wadih Ghanem
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
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Boucher M, Tellez M, Anderson JT. Differences in distress: Variance and production of American Crocodile ( Crocodylus acutus) distress calls in Belize. Ecol Evol 2020; 10:9624-9634. [PMID: 33005335 PMCID: PMC7520206 DOI: 10.1002/ece3.6556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022] Open
Abstract
Acoustic communication of American Crocodiles (Crocodylus acutus) is relatively understudied. Our overall aim was to determine the acoustic structure of wild American Crocodile distress calls, distinguish call differences among size classes (hatchling, juvenile, sub-adult, and adult), and investigate call production on a gradient of human disturbance. American Crocodile distress calls have strong frequency modulation and are comprised of multiple harmonics in a downsweeping pattern. Measured parameters (total duration, first quartile duration, maximal frequency, first quartile frequency, end frequency, slope of first quartile, slope of last quartiles) differed significantly among size classes (p < .05). Hatchling distress calls are higher in frequency and strongly modulated, whereas calls produced by sub-adults and adults showed little modulation, are lower in frequency, and have greater overall duration. Proportion of crocodiles that produced distress calls during capture differed by size class and sampling location, particularly adult distress calls which are reported here to be produced with undocumented frequency. We determined that American Crocodiles of all size classes produce distress calls at varying rates among study sites. Our results demonstrate that American crocodiles produce distress call more frequently at sites with higher anthropogenic activity. Measured call parameters of juveniles and hatchling American crocodiles also varied among sites in relation to human disturbance. Calls recorded at sites of high anthropogenic impact have increased duration and less modulation which may adversely affect response to emitted distress calls. Proportional and call parameter variances suggest anthropogenic activity as a driver for increased call production and alteration of call parameters at high human-impacted sites.
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Affiliation(s)
- Miriam Boucher
- School of Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | - Marisa Tellez
- Crocodile Research CoalitionStann CreekBelize
- Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
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Li X, Wang C, Krishnan PG. Effects of corn distillers dried grains on dough properties and quality of Chinese steamed bread. Food Sci Nutr 2020; 8:3999-4008. [PMID: 32884681 PMCID: PMC7455979 DOI: 10.1002/fsn3.1604] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 11/18/2022] Open
Abstract
Chinese steamed bread (CSB) accounts for 30% of the wheat end-use in China. CSB was studied as a platform for fiber and protein enrichment, employing corn distillers dried grains. Food grade distiller's grain (FDDG) processed from co-products from the corn ethanol industry was used as the enrichment ingredient. Since CSB uses a lean formula with little or no added sugar or fat, it relies entirely on fermentation and steaming for flavor and texture development. FDDG was used to replace 0%-25% all-purpose flour (APF) in CSB formulations. Effects of FDDG on dough properties and quality of CSB were evaluated by instrumental (Farinograph, Mixolab, and Texture Analyzer), nutritional, and sensory methods. Protein and dietary fiber contents showed significant increases to 18.8% and 15.3%, respectively, for 100 g of steamed bread (25% FDDG db). Fiber in 100 g of fresh FDDG CSB ranged from 2.8 to 7.7 g. FDDG fortified doughs demonstrated higher water absorption, while dough development time, dough stability, and dough extensibility decreased significantly with partial APF replacement. FDDG contributed to increased hardness and adhesiveness in the CSB. Crumb analysis revealed reduced number of gas cells at higher FDDG substitution. FDDG enrichment reduced brightness (L*) of flour blends and CSB. Rheological and sensory analysis showed an upper level of FDDG substitution of 15% was acceptable without detriment to dough functionality, texture, and taste.
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Affiliation(s)
- Xiaona Li
- College of Food ScienceShenyang Agricultural UniversityShenyangChina
| | - Chunyang Wang
- College of Health and Human SciencesNorth Carolina State UniversityCullowheeNCUSA
| | - Padmanaban G. Krishnan
- Department of Dairy and Food ScienceCollege of Agriculture, Food and Environmental SciencesSouth Dakota State UniversityBrookingsSDUSA
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Kenchanmane Raju SK, Adkins M, Enersen A, Santana de Carvalho D, Studer AJ, Ganapathysubramanian B, Schnable PS, Schnable JC. Leaf Angle eXtractor: A high-throughput image processing framework for leaf angle measurements in maize and sorghum. Appl Plant Sci 2020; 8:e11385. [PMID: 32999772 PMCID: PMC7507698 DOI: 10.1002/aps3.11385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/17/2020] [Indexed: 05/08/2023]
Abstract
PREMISE Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment. METHODS High-throughput time series image data from water-deprived maize (Zea mays subsp. mays) and sorghum (Sorghum bicolor) were obtained using battery-powered time-lapse cameras. A MATLAB-based image processing framework, Leaf Angle eXtractor (LAX), was developed to extract and quantify leaf angles from images of maize and sorghum plants under drought conditions. RESULTS Leaf angle measurements showed differences in leaf responses to drought in maize and sorghum. Tracking leaf angle changes at intervals as short as one minute enabled distinguishing leaves that showed signs of wilting under water deprivation from other leaves on the same plant that did not show wilting during the same time period. DISCUSSION Automating leaf angle measurements using LAX makes it feasible to perform large-scale experiments to evaluate, understand, and exploit the spatial and temporal variations in plant response to water limitations.
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Affiliation(s)
- Sunil K. Kenchanmane Raju
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Miles Adkins
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | - Alex Enersen
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
| | - Daniel Santana de Carvalho
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of BioinformaticsFederal University of Minas GeraisBelo HorizonteMinas GeraisBrazil
| | | | | | | | - James C. Schnable
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Department of Agronomy and HorticultureUniversity of Nebraska–LincolnLincolnNebraskaUSA
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Zhang L, Liao Y, Wang Y, Zhang S, Yang W, Pan X, Wang ZL. Cellulose II Aerogel-Based Triboelectric Nanogenerator. Adv Funct Mater 2020; 30:2001763. [PMID: 32684908 PMCID: PMC7357570 DOI: 10.1002/adfm.202001763] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 05/15/2023]
Abstract
Cellulose-based triboelectric nanogenerators (TENGs) have gained increasing attention. In this study, a novel method is demonstrated to synthesize cellulose-based aerogels and such aerogels are used to fabricate TENGs that can serve as mechanical energy harvesters and self-powered sensors. The cellulose II aerogel is fabricated via a dissolution-regeneration process in a green inorganic molten salt hydrate solvent (lithium bromide trihydrate), where. The as-fabricated cellulose II aerogel exhibits an interconnected open-pore 3D network structure, higher degree of flexibility, high porosity, and a high surface area of 221.3 m2 g-1. Given its architectural merits, the cellulose II aerogel-based TENG presents an excellent mechanical response sensitivity and high electrical output performance. By blending with other natural polysaccharides, i.e., chitosan and alginic acid, electron-donating and electron-withdrawing groups are introduced into the composite cellulose II aerogels, which significantly improves the triboelectric performance of the TENG. The cellulose II aerogel-based TENG is demonstrated to light up light-emitting diodes, charge commercial capacitors, power a calculator, and monitor human motions. This study demonstrates the facile fabrication of cellulose II aerogel and its application in TENG, which leads to a high-performance and eco-friendly energy harvesting and self-powered system.
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Affiliation(s)
- Lei Zhang
- School of Materials Science and EngineeringGeorgia Institute of TechnologyAtlantaGA30332‐0245USA
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education)School of Materials Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031P. R. China
| | - Yang Liao
- Department of Biological Systems EngineeringUniversity of Wisconsin‐Madison460 Henry MallMadisonWI53706USA
| | - Yi‐Cheng Wang
- Department of Food Science and Human NutritionUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Steven Zhang
- School of Materials Science and EngineeringGeorgia Institute of TechnologyAtlantaGA30332‐0245USA
| | - Weiqing Yang
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education)School of Materials Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031P. R. China
| | - Xuejun Pan
- Department of Biological Systems EngineeringUniversity of Wisconsin‐Madison460 Henry MallMadisonWI53706USA
| | - Zhong Lin Wang
- School of Materials Science and EngineeringGeorgia Institute of TechnologyAtlantaGA30332‐0245USA
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De Vries MC, Brown DA, Allen ME, Bindoff L, Gorman GS, Karaa A, Keshavan N, Lamperti C, McFarland R, Ng YS, O'Callaghan M, Pitceathly RDS, Rahman S, Russel FGM, Varhaug KN, Schirris TJJ, Mancuso M. Safety of drug use in patients with a primary mitochondrial disease: An international Delphi-based consensus. J Inherit Metab Dis 2020; 43:800-818. [PMID: 32030781 PMCID: PMC7383489 DOI: 10.1002/jimd.12196] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022]
Abstract
Clinical guidance is often sought when prescribing drugs for patients with primary mitochondrial disease. Theoretical considerations concerning drug safety in patients with mitochondrial disease may lead to unnecessary withholding of a drug in a situation of clinical need. The aim of this study was to develop consensus on safe medication use in patients with a primary mitochondrial disease. A panel of 16 experts in mitochondrial medicine, pharmacology, and basic science from six different countries was established. A modified Delphi technique was used to allow the panellists to consider draft recommendations anonymously in two Delphi rounds with predetermined levels of agreement. This process was supported by a review of the available literature and a consensus conference that included the panellists and representatives of patient advocacy groups. A high level of consensus was reached regarding the safety of all 46 reviewed drugs, with the knowledge that the risk of adverse events is influenced both by individual patient risk factors and choice of drug or drug class. This paper details the consensus guidelines of an expert panel and provides an important update of previously established guidelines in safe medication use in patients with primary mitochondrial disease. Specific drugs, drug groups, and clinical or genetic conditions are described separately as they require special attention. It is important to emphasise that consensus-based information is useful to provide guidance, but that decisions related to drug prescribing should always be tailored to the specific needs and risks of each individual patient. We aim to present what is current knowledge and plan to update this regularly both to include new drugs and to review those currently included.
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Affiliation(s)
- Maaike C. De Vries
- Radboudumc Amalia Children's HospitalRadboud Center for Mitochondrial MedicineNijmegenThe Netherlands
| | - David A. Brown
- Department of Human Nutrition, Foods, and Exercise and the Virginia Tech Center for Drug DiscoveryVirginia TechBlacksburgVirginia
| | - Mitchell E. Allen
- Department of Human Nutrition, Foods, and Exercise and the Virginia Tech Center for Drug DiscoveryVirginia TechBlacksburgVirginia
| | - Laurence Bindoff
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
| | - Gráinne S. Gorman
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- The Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Amel Karaa
- Genetics Unit, Massachusetts General HospitalHarvard Medical SchoolBostonMassachusetts
| | - Nandaki Keshavan
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
- Metabolic UnitGreat Ormond Street Hospital NHS Foundation TrustLondonUK
| | - Costanza Lamperti
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- The Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- The Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Mar O'Callaghan
- Department of Neurology, Metabolic UnitHospital Sant Joan de DéuBarcelonaSpain
- CIBERERInstituto de Salud Carlos IIIBarcelonaSpain
| | - Robert D. S. Pitceathly
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology and The National Hospital for Neurology and NeurosurgeryLondonUK
| | - Shamima Rahman
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
- Metabolic UnitGreat Ormond Street Hospital NHS Foundation TrustLondonUK
| | - Frans G. M. Russel
- Department of Pharmacology and ToxicologyRadboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, RadboudumcNijmegenThe Netherlands
| | - Kristin N. Varhaug
- Department of Clinical MedicineUniversity of BergenBergenNorway
- Department of NeurologyHaukeland University HospitalBergenNorway
| | - Tom J. J. Schirris
- Department of Pharmacology and ToxicologyRadboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, RadboudumcNijmegenThe Netherlands
| | - Michelangelo Mancuso
- Department of Clinical and Experimental Medicine, Neurological InstituteUniversity of PisaPisaItaly
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Mirnezami SV, Young T, Assefa T, Prichard S, Nagasubramanian K, Sandhu K, Sarkar S, Sundararajan S, O’Neal ME, Ganapathysubramanian B, Singh A. Automated trichome counting in soybean using advanced image-processing techniques. Appl Plant Sci 2020; 8:e11375. [PMID: 32765974 PMCID: PMC7394713 DOI: 10.1002/aps3.11375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/25/2020] [Indexed: 05/20/2023]
Abstract
PREMISE Trichomes are hair-like appendages extending from the plant epidermis. They serve many important biotic roles, including interference with herbivore movement. Characterizing the number, density, and distribution of trichomes can provide valuable insights on plant response to insect infestation and define the extent of plant defense capability. Automated trichome counting would speed up this research but poses several challenges, primarily because of the variability in coloration and the high occlusion of the trichomes. METHODS AND RESULTS We developed a simplified method for image processing for automated and semi-automated trichome counting. We illustrate this process using 30 leaves from 10 genotypes of soybean (Glycine max) differing in trichome abundance. We explored various heuristic image-processing methods including thresholding and graph-based algorithms to facilitate trichome counting. Of the two automated and two semi-automated methods for trichome counting tested and with the help of regression analysis, the semi-automated manually annotated trichome intersection curve method performed best, with an accuracy of close to 90% compared with the manually counted data. CONCLUSIONS We address trichome counting challenges including occlusion by combining image processing with human intervention to propose a semi-automated method for trichome quantification. This provides new opportunities for the rapid and automated identification and quantification of trichomes, which has applications in a wide variety of disciplines.
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Affiliation(s)
- Seyed Vahid Mirnezami
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
- Colaberry Inc.200 Portland StreetBostonMassachusetts02114USA
| | - Therin Young
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | | | | | | | - Kulbir Sandhu
- Department of AgronomyIowa State UniversityAmesIowaUSA
| | - Soumik Sarkar
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | | | | | | | - Arti Singh
- Department of AgronomyIowa State UniversityAmesIowaUSA
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Hu D, Chen Z, Zhang C, Ganiger M. Reduction of Phakopsora pachyrhizi infection on soybean through host- and spray-induced gene silencing. Mol Plant Pathol 2020; 21:794-807. [PMID: 32196911 PMCID: PMC7214474 DOI: 10.1111/mpp.12931] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 02/19/2020] [Indexed: 05/10/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate fungal pathogen Phakopsora pachyrhizi, often leads to significant yield losses and can only be managed through fungicide applications currently. In the present study, eight urediniospore germination or appressorium formation induced P. pachyrhizi genes were investigated for their feasibility to suppress ASR through a bean pod mottle virus (BPMV)-based host-induced gene silencing (HIGS) strategy. Soybean plants expressing three of these modified BPMV vectors suppressed the expression of their corresponding target gene by 45%-80%, fungal biomass accumulation by 58%-80%, and significantly reduced ASR symptom development in soybean leaves after the plants were inoculated with P. pachyrhizi, demonstrating that HIGS can be used to manage ASR. In addition, when the in vitro synthesized double-stranded RNAs (dsRNAs) for three of the genes encoding an acetyl-CoA acyltransferase, a 40S ribosomal protein S16, and glycine cleavage system H protein were sprayed directly onto detached soybean leaves prior to P. pachyrhizi inoculation, they also resulted in an average of over 73% reduction of pustule numbers and 75% reduction in P. pachyrhizi biomass accumulation on the detached leaves compared to the controls. To the best of our knowledge, this is the first report of suppressing P. pachyrhizi infection in soybean through both HIGS and spray-induced gene silencing. It was demonstrated that either HIGS constructs targeting P. pachyrhizi genes or direct dsRNA spray application could be an effective strategy for reducing ASR development on soybean.
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Affiliation(s)
- Dongfang Hu
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Zhi‐Yuan Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Chunquan Zhang
- Department of AgricultureAlcorn State UniversityLormanMSUSA
| | - Mala Ganiger
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
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Salesse‐Smith CE, Sharwood RE, Busch FA, Stern DB. Increased Rubisco content in maize mitigates chilling stress and speeds recovery. Plant Biotechnol J 2020; 18:1409-1420. [PMID: 31793172 PMCID: PMC7207003 DOI: 10.1111/pbi.13306] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/14/2019] [Indexed: 05/22/2023]
Abstract
Many C4 plants, including maize, perform poorly under chilling conditions. This phenomenon has been linked in part to decreased Rubisco abundance at lower temperatures. An exception to this is chilling-tolerant Miscanthus, which is able to maintain Rubisco protein content under such conditions. The goal of this study was to investigate whether increasing Rubisco content in maize could improve performance during or following chilling stress. Here, we demonstrate that transgenic lines overexpressing Rubisco large and small subunits and the Rubisco assembly factor RAF1 (RAF1-LSSS), which have increased Rubisco content and growth under control conditions, maintain increased Rubisco content and growth during chilling stress. RAF1-LSSS plants exhibited 12% higher CO2 assimilation relative to nontransgenic controls under control growth conditions, and a 17% differential after 2 weeks of chilling stress, although assimilation rates of all genotypes were ~50% lower in chilling conditions. Chlorophyll fluorescence measurements showed RAF1-LSSS and WT plants had similar rates of photochemical quenching during chilling, suggesting Rubisco may not be the primary limiting factor that leads to poor performance in maize under chilling conditions. In contrast, RAF1-LSSS had improved photochemical quenching before and after chilling stress, suggesting that increased Rubisco may help plants recover faster from chilling conditions. Relatively increased leaf area, dry weight and plant height observed before chilling in RAF1-LSSS were also maintained during chilling. Together, these results demonstrate that an increase in Rubisco content allows maize plants to better cope with chilling stress and also improves their subsequent recovery, yet additional modifications are required to engineer chilling tolerance in maize.
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Affiliation(s)
- Coralie E. Salesse‐Smith
- Boyce Thompson InstituteIthacaNYUSA
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Robert E. Sharwood
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Florian A. Busch
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - David B. Stern
- Boyce Thompson InstituteIthacaNYUSA
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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Gorman Z, Christensen SA, Yan Y, He Y, Borrego E, Kolomiets MV. Green leaf volatiles and jasmonic acid enhance susceptibility to anthracnose diseases caused by Colletotrichum graminicola in maize. Mol Plant Pathol 2020; 21:702-715. [PMID: 32105380 PMCID: PMC7170777 DOI: 10.1111/mpp.12924] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/08/2020] [Accepted: 01/28/2020] [Indexed: 05/20/2023]
Abstract
Colletotrichum graminicola is a hemibiotrophic fungus that causes anthracnose leaf blight (ALB) and anthracnose stalk rot (ASR) in maize. Despite substantial economic losses caused by these diseases, the defence mechanisms against this pathogen remain poorly understood. Several hormones are suggested to aid in defence against C. graminicola, such as jasmonic acid (JA) and salicylic acid (SA), but supporting genetic evidence was not reported. Green leaf volatiles (GLVs) are a group of well-characterized volatiles that induce JA biosynthesis in maize and are known to function in defence against necrotrophic pathogens. Information regarding the role of GLVs and JA in interactions with (hemi)biotrophic pathogens remains limited. To functionally elucidate GLVs and JA in defence against a hemibiotrophic pathogen, we tested GLV- and JA-deficient mutants, lox10 and opr7 opr8, respectively, for resistance to ASR and ALB and profiled jasmonates and SA in their stalks and leaves throughout infection. Both mutants were resistant and generally displayed elevated levels of SA and low amounts of jasmonates, especially at early stages of infection. Pretreatment with GLVs restored susceptibility of lox10 mutants, but not opr7 opr8 mutants, which coincided with complete rescue of JA levels. Exogenous methyl jasmonate restored susceptibility in both mutants when applied before inoculation, whereas methyl salicylate did not induce further resistance in either of the mutants, but did induce mutant-like resistance in the wild type. Collectively, this study reveals that GLVs and JA contribute to maize susceptibility to C. graminicola due to suppression of SA-related defences.
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Affiliation(s)
- Zachary Gorman
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
| | - Shawn A. Christensen
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
- Department of Agriculture–Agricultural Research Service (USDA–ARS), Chemistry Research UnitCenter for Medical, Agricultural, and Veterinary EntomologyGainesvilleFLUSA
| | - Yuanxin Yan
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Yongming He
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
- Jiangxi Key Laboratory of Crop Physiology, Ecology, and Genetic BreedingJiangxi Agricultural UniversityNanchangChina
| | - Eli Borrego
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
- Thomas H. Gosnell School of Life SciencesRochester Institute of TechnologyRochesterNYUSA
| | - Michael V. Kolomiets
- Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationTXUSA
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Rowland SD, Zumstein K, Nakayama H, Cheng Z, Flores AM, Chitwood DH, Maloof JN, Sinha NR. Leaf shape is a predictor of fruit quality and cultivar performance in tomato. New Phytol 2020; 226:851-865. [PMID: 31880321 PMCID: PMC7187315 DOI: 10.1111/nph.16403] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/14/2019] [Indexed: 05/04/2023]
Abstract
Commercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits. Here the role of leaf morphology was investigated for its impact on fruit quality. Heirloom cultivars were grown in field conditions, and BRIX by yield (BY) and other traits were measured over a 14-wk period. The complex relationships among these morphological and physiological traits were evaluated using partial least-squares path modeling, and a consensus model was developed. Photosynthesis contributed strongly to vegetative biomass and sugar content of fruits but had a negative impact on yield. Conversely leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield. Cultivars such as Stupice and Glacier, with very round leaves, had the highest performance in both fruit sugar and yield. Our model accurately predicted BY for two commercial cultivars using leaf shape data as input. This study revealed the importance of leaf shape to fruit quality in tomato, with rounder leaves having significantly improved fruit quality. This correlation was maintained across a range of diverse genetic backgrounds and shows the importance of leaf morphology in tomato crop improvement.
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Affiliation(s)
| | | | - Hokuto Nakayama
- Department of Plant BiologyUniversity of CaliforniaDavisCA95616USA
- Gradute School of ScienceUniversity of TokyoHongo Bunkyo‐kuTokyo113‐0033Japan
| | - Zizhang Cheng
- College of ScienceSichuan Agriculture UniversityYaanSichuan Province625014China
| | - Amber M. Flores
- Department of Plant BiologyUniversity of CaliforniaDavisCA95616USA
| | - Daniel H. Chitwood
- Department of Plant BiologyUniversity of CaliforniaDavisCA95616USA
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
| | - Julin N. Maloof
- Department of Plant BiologyUniversity of CaliforniaDavisCA95616USA
| | - Neelima R. Sinha
- Department of Plant BiologyUniversity of CaliforniaDavisCA95616USA
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45
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Attaran E, Berim A, Killiny N, Beyenal H, Gang DR, Omsland A. Controlled replication of 'Candidatus Liberibacter asiaticus' DNA in citrus leaf discs. Microb Biotechnol 2020; 13:747-759. [PMID: 31958876 PMCID: PMC7111093 DOI: 10.1111/1751-7915.13531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/13/2022] Open
Abstract
'Candidatus Liberibacter asiaticus' is a fastidious bacterium and a putative agent of citrus greening disease (a.k.a., huanglongbing, HLB), a significant agricultural disease that affects citrus fruit quality and tree health. In citrus, 'Ca. L. asiaticus' is phloem limited. Lack of culture tools to study 'Ca. L. asiaticus' complicates analysis of this important organism. To improve understanding of 'Ca. L. asiaticus'-host interactions including parameters that affect 'Ca. L. asiaticus' replication, methods suitable for screening pathogen responses to physicochemical and nutritional variables are needed. We describe a leaf disc-based culture assay that allows highly selective measurement of changes in 'Ca. L. asiaticus' DNA within plant tissue incubated under specific physicochemical and nutritional conditions. qPCR analysis targeting the hypothetical gene CD16-00155 (strain A4) allowed selective quantification of 'Ca. L. asiaticus' DNA content within infected tissue. 'Ca. L. asiaticus' DNA replication was observed in response to glucose exclusively under microaerobic conditions, and the antibiotic amikacin further enhanced 'Ca. L. asiaticus' DNA replication. Metabolite profiling revealed a moderate impact of 'Ca. L. asiaticus' on the ability of leaf tissue to metabolize and respond to glucose.
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Affiliation(s)
- Elham Attaran
- Paul G. Allen School for Global Animal HealthWashington State UniversityPullmanWAUSA
| | - Anna Berim
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Nabil Killiny
- Plant Pathology DepartmentCitrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
| | - Haluk Beyenal
- Gene and Linda Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWAUSA
| | - David R. Gang
- Institute of Biological ChemistryWashington State UniversityPullmanWAUSA
| | - Anders Omsland
- Paul G. Allen School for Global Animal HealthWashington State UniversityPullmanWAUSA
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Thapa SP, De Francesco A, Trinh J, Gurung FB, Pang Z, Vidalakis G, Wang N, Ancona V, Ma W, Coaker G. Genome-wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors. Mol Plant Pathol 2020; 21:716-731. [PMID: 32108417 PMCID: PMC7170780 DOI: 10.1111/mpp.12925] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
'Candidatus Liberibacter' species are insect-transmitted, phloem-limited α-Proteobacteria in the order of Rhizobiales. The citrus industry is facing significant challenges due to huanglongbing, associated with infection from 'Candidatus Liberibacter asiaticus' (Las). In order to gain greater insight into 'Ca. Liberibacter' biology and genetic diversity, we have performed genome sequencing and comparative analyses of diverse 'Ca. Liberibacter' species, including those that can infect citrus. Our phylogenetic analysis differentiates 'Ca. Liberibacter' species and Rhizobiales in separate clades and suggests stepwise evolution from a common ancestor splitting first into nonpathogenic Liberibacter crescens followed by diversification of pathogenic 'Ca. Liberibacter' species. Further analysis of Las genomes from different geographical locations revealed diversity among isolates from the United States. Our phylogenetic study also indicates multiple Las introduction events in California and spread of the pathogen from Florida to Texas. Texan Las isolates were closely related, while Florida and Asian isolates exhibited the most genetic variation. We have identified conserved Sec translocon (SEC)-dependent effectors likely involved in bacterial survival and virulence of Las and analysed their expression in their plant host (citrus) and insect vector (Diaphorina citri). Individual SEC-dependent effectors exhibited differential expression patterns between host and vector, indicating that Las uses its effector repertoire to differentially modulate diverse organisms. Collectively, this work provides insights into the evolution of 'Ca. Liberibacter' species, the introduction of Las in the United States and identifies promising Las targets for disease management.
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Affiliation(s)
- Shree P. Thapa
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Agustina De Francesco
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Jessica Trinh
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Fatta B. Gurung
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Zhiqian Pang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Georgios Vidalakis
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Veronica Ancona
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Wenbo Ma
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Gitta Coaker
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
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47
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Ony MA, Nowicki M, Boggess SL, Klingeman WE, Zobel JM, Trigiano RN, Hadziabdic D. Habitat fragmentation influences genetic diversity and differentiation: Fine-scale population structure of Cercis canadensis (eastern redbud). Ecol Evol 2020; 10:3655-3670. [PMID: 32313625 PMCID: PMC7160182 DOI: 10.1002/ece3.6141] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 02/05/2023] Open
Abstract
Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen-seed dispersal mechanisms. However, in the case of tree species, effective pollen-seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine-scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the genetic diversity and population structure of Cercis canadensis L. (eastern redbud) wild populations on a fine scale within fragmented areas centered around the borders of Georgia-Tennessee, USA. We hypothesized high genetic diversity among the collections of C. canadensis distributed across smaller geographical ranges. Fifteen microsatellite loci were used to genotype 172 individuals from 18 unmanaged and naturally occurring collection sites. Our results indicated presence of population structure, overall high genetic diversity (H E = 0.63, H O = 0.34), and moderate genetic differentiation (F ST = 0.14) among the collection sites. Two major genetic clusters within the smaller geographical distribution were revealed by STRUCTURE. Our data suggest that native C. canadensis populations in the fragmented area around the Georgia-Tennessee border were able to maintain high levels of genetic diversity, despite the presence of considerable spatial genetic structure. As habitat isolation may negatively affect gene flow of outcrossing species across time, consequences of habitat fragmentation should be regularly monitored for this and other forest species. This study also has important implications for habitat management efforts and future breeding programs.
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Affiliation(s)
- Meher A. Ony
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Marcin Nowicki
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Sarah L. Boggess
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | | | - John M. Zobel
- Department of Forest ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Robert N. Trigiano
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
| | - Denita Hadziabdic
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTNUSA
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48
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Gray SB, Rodriguez‐Medina J, Rusoff S, Toal TW, Kajala K, Runcie DE, Brady SM. Translational regulation contributes to the elevated CO 2 response in two Solanum species. Plant J 2020; 102:383-397. [PMID: 31797460 PMCID: PMC7216843 DOI: 10.1111/tpj.14632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 05/12/2023]
Abstract
Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .
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Affiliation(s)
- Sharon B. Gray
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Joel Rodriguez‐Medina
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Samuel Rusoff
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Ted W. Toal
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
- Present address:
Plant EcophysiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Daniel E. Runcie
- Department of Plant SciencesUniversity of California, DavisOne Shields AvenueDavisCA95616USA
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
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49
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Hunter JE, Gannon TW, Richardson RJ, Yelverton FH, Leon RG. Integration of remote-weed mapping and an autonomous spraying unmanned aerial vehicle for site-specific weed management. Pest Manag Sci 2020; 76:1386-1392. [PMID: 31622004 PMCID: PMC7064951 DOI: 10.1002/ps.5651] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Unmanned aerial vehicles (UAVs) have been used in agriculture to collect imagery for crop and pest monitoring, and for decision-making purposes. Spraying-capable UAVs are now commercially available worldwide for agricultural applications. Combining UAV weed mapping and UAV sprayers into an UAV integrated system (UAV-IS) can offer a new alternative to implement site-specific pest management. RESULTS The UAV-IS was 0.3- to 3-fold more efficient at identifying and treating target weedy areas, while minimizing treatment on non-weedy areas, than ground-based broadcast applications. The UAV-IS treated 20-60% less area than ground-based broadcast applications, but also missed up to 26% of the target weedy area, while broadcast applications covered almost the entire experimental area and only missed 2-3% of the target weeds. The efficiency of UAV-IS management practices increased as weed spatial aggregation increased (patchiness). CONCLUSION Integrating UAV imagery for pest mapping and UAV sprayers can provide a new strategy for integrated pest management programs to improve efficiency and efficacy while reducing the amount of pesticide being applied. The UAV-IS has the potential to improve the detection and control of weed escapes to reduce/delay herbicide resistance evolution. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Joseph E Hunter
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Travis W Gannon
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Robert J Richardson
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Fred H Yelverton
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Ramon G Leon
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
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50
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Sapkota S, Mergoum M, Liu Z. The translucens group of Xanthomonas translucens: Complicated and important pathogens causing bacterial leaf streak on cereals. Mol Plant Pathol 2020; 21:291-302. [PMID: 31967397 PMCID: PMC7036361 DOI: 10.1111/mpp.12909] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 12/21/2019] [Indexed: 05/31/2023]
Abstract
UNLABELLED Xanthomonas translucens is a group of gram-negative bacteria that can cause important diseases in cereal crops and forage grasses. Different pathovars have been defined according to their host ranges, and molecular and biochemical characteristics. Pathovars have been placed into two major groups: translucens and graminis. The translucens group contains the pathovars causing bacterial leaf streak (BLS) on cereal crops such as wheat, barley, triticale, rye, and oat. In recent years, BLS has re-emerged as a major problem for many wheat- and barley-producing areas worldwide. The biology of the pathogens and the host-pathogen interactions in cereal BLS diseases were poorly understood. However, recent genome sequence data have provided an insight into the bacterial phylogeny and identification and pathogenicity/virulence. Furthermore, identification of sources of resistance to BLS and mapping of the resistance genes have been initiated. TAXONOMY Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. translucens; translucens group pathovars: undulosa, translucens, cerealis, hordei, and secalis; graminis group pathovars: arrhenatheri, graminis, poae, phlei; newly established pathovar: pistaciae. HOST RANGE X. translucens mainly infects plant species in the Poaceae with the translucens group on cereal crop species and the graminis group on forage grass species. However, some strains have been isolated from, and are able to infect, ornamental asparagus and pistachio trees. Most pathovars have a narrow host range, while a few can infect a broad range of hosts. GENOME The complete genome sequence is available for two X. translucens pv. undulosa strains and one pv. translucens strain. A draft genome sequence is also available for at least one strain from each pathovar. The X. translucens pv. undulosa strain Xt4699 was the first to have its complete genome sequenced, which consists of 4,561,137 bp with total GC content approximately at 68% and 3,528 predicted genes. VIRULENCE MECHANISMS Like most xanthomonads, X. translucens utilizes a type III secretion system (T3SS) to deliver a suite of T3SS effectors (T3Es) inside plant cells. Transcription activator-like effectors, a special group of T3Es, have been identified in most of the X. translucens genomes, some of which have been implicated in virulence. Genetic factors determining host range virulence have also been identified.
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Affiliation(s)
- Suraj Sapkota
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
- Department of Crop and Soil SciencesUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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