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Fielder H, Beale T, Jeger MJ, Oliver G, Parnell S, Szyniszewska AM, Taylor P, Cunniffe NJ. A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2022. PHYTOPATHOLOGY 2024; 114:1717-1732. [PMID: 38723169 DOI: 10.1094/phyto-01-24-0042-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
This scientometric study reviews the scientific literature and CABI distribution records published in 2022 to find evidence of major disease outbreaks and first reports of pathogens in new locations or on new hosts. This is the second time we have done this, and this study builds on our work documenting and analyzing reports from 2021. Pathogens with three or more articles identified in 2022 literature were Xylella fastidiosa, Bursaphelenchus xylophilus, Meloidogyne species complexes, 'Candidatus Liberibacter asiaticus', Raffaelea lauricola, Fusarium oxysporum formae specialis, and Puccinia graminis f. sp. tritici. Our review of CABI distribution records found 29 pathogens with confirmed first reports in 2022. Pathogens with four or more first reports were Meloidogyne species complexes, Pantoea ananatis, grapevine red globe virus, and Thekopsora minima. Analysis of the proportion of new distribution records from 2022 indicated that grapevine red globe virus, sweet potato chlorotic stunt virus, and 'Ca. Phytoplasma vitis' may have been actively spreading. As we saw last year, there was little overlap between the pathogens identified by reviewing scientific literature versus distribution records. We hypothesize that this lack of concordance is because of the unavoidable lag between first reports of the type reported in the CABI database of a pathogen in a new location and any subsequent major disease outbreaks being reported in the scientific literature, particularly because the latter depends on the journal policy on types of papers to be considered, whether the affected crop is major or minor, and whether the pathogen is of current scientific interest. Strikingly, too, there was also no overlap between species assessed to be actively spreading in this year's study and those identified last year. We hypothesize that this is because of inconsistencies in sampling coverage and effort over time and delays between the first arrival of a pathogen in a new location and its first report, particularly for certain classes of pathogens causing only minor or non-economically damaging symptoms, which may have been endemic for some time before being reported. In general, introduction of new pathogens and outbreaks of extant pathogens threaten food security and ecosystem services. Continued monitoring of these threats is essential to support phytosanitary measures intended to prevent pathogen introductions and management of threats within a country.
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Affiliation(s)
| | - Tim Beale
- CABI, Nosworthy Way, Wallingford, U.K
| | - Michael J Jeger
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, U.K
| | | | - Stephen Parnell
- School of Life Sciences, University of Warwick, Coventry, U.K
| | | | | | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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Roman-Reyna V, Crandall SG. Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease. FRONTIERS IN PLANT SCIENCE 2024; 15:1405042. [PMID: 39055364 PMCID: PMC11269093 DOI: 10.3389/fpls.2024.1405042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, United States
| | - Sharifa G. Crandall
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, United States
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Etherton BA, Choudhury RA, Alcalá Briseño RI, Mouafo-Tchinda RA, Plex Sulá AI, Choudhury M, Adhikari A, Lei SL, Kraisitudomsook N, Buritica JR, Cerbaro VA, Ogero K, Cox CM, Walsh SP, Andrade-Piedra JL, Omondi BA, Navarrete I, McEwan MA, Garrett KA. Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters. PHYTOPATHOLOGY 2024; 114:855-868. [PMID: 38593748 DOI: 10.1094/phyto-03-24-0079-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Berea A Etherton
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Robin A Choudhury
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Edinburg, TX, U.S.A
| | - Ricardo I Alcalá Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Romaric A Mouafo-Tchinda
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Aaron I Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Manoj Choudhury
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Ashish Adhikari
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Si Lin Lei
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Nattapol Kraisitudomsook
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Chom Bueng, Ratchaburi, Thailand
| | - Jacobo Robledo Buritica
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Vinicius A Cerbaro
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL, U.S.A
| | - Kwame Ogero
- International Potato Center (CIP), Mwanza, Tanzania
| | - Cindy M Cox
- USAID Bureau for Humanitarian Assistance, Washington, DC, U.S.A
| | - Stephen P Walsh
- USAID Bureau for Humanitarian Assistance, Washington, DC, U.S.A
| | | | | | | | - Margaret A McEwan
- International Potato Center (CIP) Africa Regional Office, Nairobi, Kenya
- Wageningen University and Research, Wageningen, the Netherlands
| | - Karen A Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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Wang M, Peng X, Wang C, Tang X. Identification of two plastid transit peptides for construction of pollen-inactivation system in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:33. [PMID: 38694254 PMCID: PMC11058180 DOI: 10.1007/s11032-024-01471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/22/2024] [Indexed: 05/04/2024]
Abstract
Hybrid seed production technology (SPT) is achieved through the utilization of a recessive nuclear male-sterile mutant transformed with a transgenic cassette comprising three essential components: the wild-type gene to restore the fertility of the male-sterile mutant, an α-amylase gene to disrupt transgenic pollen grains, and red fluorescence protein gene DsRed to distinguish the transgenic seeds from the nontransgenic male sterile seeds. In rice, we establish the pollen disruption system by introducing an amyloplast targeting signal peptide (ASP) at the N-terminus of maize α-amylase protein ZM-AA1ΔSP (ZM-AA1 with the N-terminal signal peptide removed). The ASP facilitates the transport of ZM-AA1ΔSP protein into amyloplast where it degrades starch, resulting in disruption of the pollen fertility. To obtain such signal peptides for rice, we searched the rice proteins homologous to the defined wheat amyloplast proteins followed by protein-protein interaction network predictions and targeting signal peptides prediction. These analyses enabled the identification of four candidate ASPs in rice, which were designated as ASP1, ASP2, ASP3, and ASP4, respectively. ASP1 and ASP2, when linked with ZM-AA1ΔSP, exhibited the capability to disrupt transgenic pollen grains, whereas ASP3 and ASP4 did not produce this effect. Interestingly, the localization experiments showed that ASP3 and ASP4 were able to target the proteins into chloroplast. The ASP1 and ASP2 sequences provide valuable tools for genetic engineering of the rice male-sterile system, which will contribute to the hybrid rice breeding and production. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01471-y.
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Affiliation(s)
- Menglong Wang
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoqun Peng
- School of Life Sciences, Huizhou University, Huizhou, 516007 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Changjian Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Xiaoyan Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107 China
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Rippa M, Di Mola I, Ottaiano L, Cozzolino E, Mormile P, Mori M. Infrared Thermography Monitoring of Durum and Common Wheat for Adaptability Assessing and Yield Performance Prediction. PLANTS (BASEL, SWITZERLAND) 2024; 13:836. [PMID: 38592920 PMCID: PMC10974194 DOI: 10.3390/plants13060836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Wheat is one of the most cultivated cereals thanks to both its nutritional value and its versatility to technological transformation. Nevertheless, the growth and yield of wheat, as well as of the other food crops, can be strongly limited by many abiotic and biotic stress factors. To face this need, new methodological approaches are required to optimize wheat cultivation from both a qualitative and quantitative point of view. In this context, crop analysis based on imaging techniques has become an important tool in agriculture. Thermography is an appealing method that represents an outstanding approach in crop monitoring, as it is well suited to the emerging needs of the precision agriculture management strategies. In this work, we performed an on-field infrared monitoring of several durum and common wheat varieties to evaluate their adaptability to the internal Mediterranean area chosen for cultivation. Two new indices based on the thermal data useful to estimate the agronomical response of wheat subjected to natural stress conditions during different phenological stages of growth have been introduced. The comparison with some productive parameters collected at harvest highlighted the correlation of the indices with the wheat yield (ranging between p < 0.001 and p < 0.05), providing interesting information for their early prediction.
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Affiliation(s)
- Massimo Rippa
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello” of National Research Council of Italy (CNR ISASI), Via Campi Flegrei 34, 80072 Pozzuoli, Naples, Italy;
| | - Ida Di Mola
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy; (I.D.M.); (L.O.); (M.M.)
| | - Lucia Ottaiano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy; (I.D.M.); (L.O.); (M.M.)
| | - Eugenio Cozzolino
- Council for Agricultural Research and Economics (CREA)—Research Center for Cereal and Industrial Crops, 81100 Caserta, Italy;
| | - Pasquale Mormile
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello” of National Research Council of Italy (CNR ISASI), Via Campi Flegrei 34, 80072 Pozzuoli, Naples, Italy;
| | - Mauro Mori
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy; (I.D.M.); (L.O.); (M.M.)
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Bhoite R, Han Y, Chaitanya AK, Varshney RK, Sharma DL. Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat. THE PLANT GENOME 2024; 17:e20358. [PMID: 37265088 DOI: 10.1002/tpg2.20358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.
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Affiliation(s)
- Roopali Bhoite
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Yong Han
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Alamuru Krishna Chaitanya
- Grains Genetics Portfolio, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Darshan Lal Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
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Roman-Reyna V, Sharma A, Toth H, Konkel Z, Omiotek N, Murthy S, Faith S, Slot J, Peduto Hand F, Goss EM, Jacobs JM. Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems 2024; 9:e0079523. [PMID: 38275768 PMCID: PMC10878067 DOI: 10.1128/msystems.00795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums (Pelargonium × hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation and all contained a single plasmid (p93). Time tree and single nucleotide polymorphism whole-genome analysis estimated that Xhp2022 emerged within the last decade. The phylogenomic analysis determined that p93 resulted from the cointegration of three plasmids (p31, p45, and p66) found sporadically across isolates from previous outbreaks. Although p93 had a 49 kb nucleotide reduction, it retained putative fitness genes, which became predominant in the 2022 outbreak. Overall, we demonstrated, through rapid whole-genome sequencing and analysis, a recent, traceable event of genome reduction for niche adaptation typically observed over millennia in obligate and fastidious pathogens.IMPORTANCEThe geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has three distinct plasmids. In 2012, we found all three plasmids in individual Xhp isolates. However, in 2022, the three plasmids co-integrated into one plasmid named p93. p93 retained putative fitness genes but lost extraneous genomic material. Our findings show that the 2022 strain group of the bacterial plant pathogen Xanthomonas hortorum underwent a plasmid reduction. We also observed several Xanthomonas species from different years, hosts, and continents have similar plasmids to p93, possibly due to shared agricultural settings. We noticed parallels between genome efficiency and reduction that we see across millennia with obligate parasites with increased niche specificity.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Nicolle Omiotek
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shashanka Murthy
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Seth Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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Wang Z, Qiao X, Wang Y, Yu H, Mu C. IoT-based system of prevention and control for crop diseases and insect pests. FRONTIERS IN PLANT SCIENCE 2024; 15:1323074. [PMID: 38371415 PMCID: PMC10870423 DOI: 10.3389/fpls.2024.1323074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Environmentally friendly technologies for the prevention and control of crop diseases and insect pests are important to reduce the use of chemical pesticides, improve the quality of agricultural products, protect the environment, and promote sustainable development of crop production. On the basis of Internet of Things (IoT) technology, we developed a prevention and control system for crop diseases and insect pests with two main components: a plant protection device (the hardware) and an information management system (the software). To be suitable for both facility- and field-based production scenarios, we incorporated two types of plant protection devices, utilizing ozone sterilization and light-trap technologies. The devices were equipped with various sensors to realize real-time collection and monitoring of data on the crop production environment. The information management system has an IoT-based architecture and includes a mobile device app to enable remote control of the plant protection devices for intelligent management of plant protection data. The system can achieve efficient management of large-scale equipment applications and multi-device collaborative work to prevent and control pests and diseases. The developed system has operated successfully for several years in China and has been applied to cucumber, tomato, rice, and other crops. We demonstrate the effectiveness and practicality of the system in a greenhouse facility and in the field.
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Affiliation(s)
- Zhibin Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center of Agricultural Internet of Things, Beijing, China
| | - Xiaojun Qiao
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center of Agricultural Internet of Things, Beijing, China
| | - Ying Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center of Agricultural Internet of Things, Beijing, China
| | - Hao Yu
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center of Agricultural Internet of Things, Beijing, China
| | - Cuixia Mu
- College of Data Science and Information Technology, China Women’s University, Beijing, China
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Dong X, Zhao K, Wang Q, Wu X, Huang Y, Wu X, Zhang T, Dong Y, Gao Y, Chen P, Liu Y, Chen D, Wang S, Yang X, Yang J, Wang Y, Gao Z, Wu X, Bai Q, Li S, Hao G. PlantPAD: a platform for large-scale image phenomics analysis of disease in plant science. Nucleic Acids Res 2024; 52:D1556-D1568. [PMID: 37897364 PMCID: PMC10767946 DOI: 10.1093/nar/gkad917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/21/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
Plant disease, a huge burden, can cause yield loss of up to 100% and thus reduce food security. Actually, smart diagnosing diseases with plant phenomics is crucial for recovering the most yield loss, which usually requires sufficient image information. Hence, phenomics is being pursued as an independent discipline to enable the development of high-throughput phenotyping for plant disease. However, we often face challenges in sharing large-scale image data due to incompatibilities in formats and descriptions provided by different communities, limiting multidisciplinary research exploration. To this end, we build a Plant Phenomics Analysis of Disease (PlantPAD) platform with large-scale information on disease. Our platform contains 421 314 images, 63 crops and 310 diseases. Compared to other databases, PlantPAD has extensive, well-annotated image data and in-depth disease information, and offers pre-trained deep-learning models for accurate plant disease diagnosis. PlantPAD supports various valuable applications across multiple disciplines, including intelligent disease diagnosis, disease education and efficient disease detection and control. Through three applications of PlantPAD, we show the easy-to-use and convenient functions. PlantPAD is mainly oriented towards biologists, computer scientists, plant pathologists, farm managers and pesticide scientists, which may easily explore multidisciplinary research to fight against plant diseases. PlantPAD is freely available at http://plantpad.samlab.cn.
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Affiliation(s)
- Xinyu Dong
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Kejun Zhao
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Qi Wang
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
- Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Text Computing & Cognitive Intelligence Engineering Research Center of National Education Ministry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Xingcai Wu
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yuanqin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Xue Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Tianhan Zhang
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yawen Dong
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Yangyang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Panfeng Chen
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yingwei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Dongyu Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Shuang Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Xiaoyan Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Jing Yang
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yong Wang
- Department of Plant Pathology, Agriculture College, Guizhou University, Guiyang 550025, Guizhou, China
| | - Zhenran Gao
- New Rural Development Research Institute, Guizhou University, Guiyang 550025, Guizhou, China
| | - Xian Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Qingrong Bai
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Shaobo Li
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Gefei Hao
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
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10
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Hayman DT, Adisasmito WB, Almuhairi S, Behravesh CB, Bilivogui P, Bukachi SA, Casas N, Becerra NC, Charron DF, Chaudhary A, Ciacci Zanella JR, Cunningham AA, Dar O, Debnath N, Dungu B, Farag E, Gao GF, Khaitsa M, Machalaba C, Mackenzie JS, Markotter W, Mettenleiter TC, Morand S, Smolenskiy V, Zhou L, Koopmans M. Developing One Health surveillance systems. One Health 2023; 17:100617. [PMID: 38024258 PMCID: PMC10665171 DOI: 10.1016/j.onehlt.2023.100617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 12/01/2023] Open
Abstract
The health of humans, domestic and wild animals, plants, and the environment are inter-dependent. Global anthropogenic change is a key driver of disease emergence and spread and leads to biodiversity loss and ecosystem function degradation, which are themselves drivers of disease emergence. Pathogen spill-over events and subsequent disease outbreaks, including pandemics, in humans, animals and plants may arise when factors driving disease emergence and spread converge. One Health is an integrated approach that aims to sustainably balance and optimize human, animal and ecosystem health. Conventional disease surveillance has been siloed by sectors, with separate systems addressing the health of humans, domestic animals, cultivated plants, wildlife and the environment. One Health surveillance should include integrated surveillance for known and unknown pathogens, but combined with this more traditional disease-based surveillance, it also must include surveillance of drivers of disease emergence to improve prevention and mitigation of spill-over events. Here, we outline such an approach, including the characteristics and components required to overcome barriers and to optimize an integrated One Health surveillance system.
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Affiliation(s)
- One Health High-Level Expert Panel (OHHLEP)
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- University of Indonesia, West Java, Indonesia
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
- Centres for Disease Control and Prevention, Atlanta, GA, United States of America
- World Health Organization, Guinea Country Office, Conakry, Guinea
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
- School of Agricultural Sciences, Universidad de La Salle, Bogotá, Colombia
- Visiting Professor, One Health Institute, University of Guelph, Guelph Ontario, Canada
- Department of Civil Engineering, Indian Institute of Technology (IIT) Kanpur, India
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Swine and Poultry, Santa Catarina, Brazil
- Institute of Zoology, Zoological Society of London, United Kingdom
- Global Operations Division, United Kingdom Health Security Agency, London, United Kingdom
- Global Health Programme, Chatham House, Royal Institute of International Affairs, London, United Kingdom
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
- One Health, Bangladesh
- Afrivet B M, Pretoria, South Africa
- Qatar Ministry of Public Health (MOPH), Health Protection & Communicable Diseases Division, Doha, Qatar
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- Mississippi State University, Starkville, MS, United States of America
- EcoHealth Alliance, New York, United States of America
- Faculty of Health Sciences, Curtin University, Perth, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, South Africa
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Germany
- MIVEGEC, CNRS-IRD-Montpellier, Montpellier University, Montpelier, France
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
- Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russian Federation
- Erasmus MC, Department of Viroscience, Rotterdam, the Netherlands
| | - David T.S. Hayman
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | | | - Salama Almuhairi
- National Emergency Crisis and Disasters Management Authority, Abu Dhabi, United Arab Emirates
| | | | - Pépé Bilivogui
- World Health Organization, Guinea Country Office, Conakry, Guinea
| | - Salome A. Bukachi
- Institute of Anthropology, Gender and African Studies, University of Nairobi, Nairobi, Kenya
| | - Natalia Casas
- National Ministry of Health, Autonomous City of Buenos Aires, Argentina
| | | | - Dominique F. Charron
- Visiting Professor, One Health Institute, University of Guelph, Guelph Ontario, Canada
| | - Abhishek Chaudhary
- Department of Civil Engineering, Indian Institute of Technology (IIT) Kanpur, India
| | - Janice R. Ciacci Zanella
- Brazilian Agricultural Research Corporation (Embrapa), Embrapa Swine and Poultry, Santa Catarina, Brazil
| | | | - Osman Dar
- Global Operations Division, United Kingdom Health Security Agency, London, United Kingdom
- Global Health Programme, Chatham House, Royal Institute of International Affairs, London, United Kingdom
| | - Nitish Debnath
- Fleming Fund Country Grant to Bangladesh, DAI Global, Dhaka, Bangladesh
- One Health, Bangladesh
| | | | - Elmoubasher Farag
- Qatar Ministry of Public Health (MOPH), Health Protection & Communicable Diseases Division, Doha, Qatar
| | - George F. Gao
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Margaret Khaitsa
- Mississippi State University, Starkville, MS, United States of America
| | | | - John S. Mackenzie
- Faculty of Health Sciences, Curtin University, Perth, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, South Africa
| | | | - Serge Morand
- MIVEGEC, CNRS-IRD-Montpellier, Montpellier University, Montpelier, France
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Vyacheslav Smolenskiy
- Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russian Federation
| | - Lei Zhou
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Marion Koopmans
- Erasmus MC, Department of Viroscience, Rotterdam, the Netherlands
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11
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Wen T, Li JH, Wang Q, Gao YY, Hao GF, Song BA. Thermal imaging: The digital eye facilitates high-throughput phenotyping traits of plant growth and stress responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165626. [PMID: 37481085 DOI: 10.1016/j.scitotenv.2023.165626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Plant phenotyping is important for plants to cope with environmental changes and ensure plant health. Imaging techniques are perceived as the most critical and reliable tools for studying plant phenotypes. Thermal imaging has opened up new opportunities for nondestructive imaging of plant phenotyping. However, a comprehensive summary of thermal imaging in plant phenotyping is still lacking. Here we discuss the progress and future prospects of thermal imaging for assessing plant growth and stress responses. First, we classify thermal imaging into ground-based and aerial platforms based on their adaptability to different experimental environments (including laboratory, greenhouse, and field). It is convenient to collect phenotypic information of different dimensions. Second, in order to enhance the efficiency of thermal image processing, automatic algorithms based on deep learning are employed instead of traditional manual methods, greatly reducing the time cost of experiments. Considering its ease of implementation, handling and instant response, thermal imaging has been widely used in research on environmental stress, crop yield, and seed vigor. We have found that thermal imaging can detect thermal energy dissipation caused by living organisms (e.g., pests, viruses, bacteria, fungi, and oomycetes), enabling early disease diagnosis. It also recognizes changes leaf surface temperatures resulting from reduced transpiration rates caused by nutrient deficiency, drought, salinity, or freezing. Furthermore, thermal imaging predicts crop yield under different water states and forecasts the viability of dormant seeds after water absorption by monitoring temperature changes in the seeds. This work will assist biologists and agronomists in studying plant phenotypes and serve a guide for breeders to develop high-yielding, stress-tolerant, and superior crops.
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Affiliation(s)
- Ting Wen
- National Key Laboratory of Green Pesticide, State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Jian-Hong Li
- National Key Laboratory of Green Pesticide, State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Qi Wang
- State Key Laboratory of Public Big Data, Guizhou University, Guiyang 550025, PR China.
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China; Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.
| | - Bao-An Song
- National Key Laboratory of Green Pesticide, State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
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12
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Haile JK, Sertse D, N’Diaye A, Klymiuk V, Wiebe K, Ruan Y, Chawla HS, Henriquez MA, Wang L, Kutcher HR, Steiner B, Buerstmayr H, Pozniak CJ. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1182548. [PMID: 37900749 PMCID: PMC10601657 DOI: 10.3389/fpls.2023.1182548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.
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Affiliation(s)
- Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Demissew Sertse
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Valentyna Klymiuk
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Krystalee Wiebe
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Harmeet S. Chawla
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maria-Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Lipu Wang
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hadley R. Kutcher
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Barbara Steiner
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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13
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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14
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Wang X, Han L, Li J, Shang X, Liu Q, Li L, Zhang H. Next-generation bulked segregant analysis for Breeding 4.0. Cell Rep 2023; 42:113039. [PMID: 37651230 DOI: 10.1016/j.celrep.2023.113039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/11/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qian Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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15
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Zhang T, Zeng Q, Ji F, Wu H, Ledesma-Amaro R, Wei Q, Yang H, Xia X, Ren Y, Mu K, He Q, Kang Z, Deng R. Precise in-field molecular diagnostics of crop diseases by smartphone-based mutation-resolved pathogenic RNA analysis. Nat Commun 2023; 14:4327. [PMID: 37468480 PMCID: PMC10356797 DOI: 10.1038/s41467-023-39952-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Molecular diagnostics for crop diseases can guide the precise application of pesticides, thereby reducing pesticide usage while improving crop yield, but tools are lacking. Here, we report an in-field molecular diagnostic tool that uses a cheap colorimetric paper and a smartphone, allowing multiplexed, low-cost, rapid detection of crop pathogens. Rapid nucleic acid amplification-free detection of pathogenic RNA is achieved by combining toehold-mediated strand displacement with a metal ion-mediated urease catalysis reaction. We demonstrate multiplexed detection of six wheat pathogenic fungi and an early detection of wheat stripe rust. When coupled with a microneedle for rapid nucleic acid extraction and a smartphone app for results analysis, the sample-to-result test can be completed in ~10 min in the field. Importantly, by detecting fungal RNA and mutations, the approach allows to distinguish viable and dead pathogens and to sensitively identify mutation-carrying fungicide-resistant isolates, providing fundamental information for precision crop disease management.
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Affiliation(s)
- Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Fan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Honghong Wu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27696, USA
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Keqing Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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16
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Jeger MJ, Fielder H, Beale T, Szyniszewska AM, Parnell S, Cunniffe NJ. What Can Be Learned by a Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021? PHYTOPATHOLOGY 2023; 113:1141-1158. [PMID: 36935375 DOI: 10.1094/phyto-02-23-0069-ia] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across more than 40 host species on six continents. Pathogen species with more than five articles were Bursaphelenchus xylophilus, 'Candidatus Liberibacter asiaticus', cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, F. oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs., Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, 'Ca. Liberibacter asiaticus', citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, F. oxysporum f. sp. cubense Tropical race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, four pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens-tomato brown rugose fruit virus and cucurbit chlorotic yellows virus-to be actively emerging in/spreading to new locations. Although three important pathogens-'Ca. Liberibacter asiaticus', citrus tristeza virus, and F. oxysporum f. sp. cubense-were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general, our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Michael J Jeger
- Department of Life Sciences, Imperial College London, Ascot, U.K
| | | | | | | | - Stephen Parnell
- Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, U.K
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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17
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Terentev A, Dolzhenko V. Can Metabolomic Approaches Become a Tool for Improving Early Plant Disease Detection and Diagnosis with Modern Remote Sensing Methods? A Review. SENSORS (BASEL, SWITZERLAND) 2023; 23:5366. [PMID: 37420533 DOI: 10.3390/s23125366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 07/09/2023]
Abstract
The various areas of ultra-sensitive remote sensing research equipment development have provided new ways for assessing crop states. However, even the most promising areas of research, such as hyperspectral remote sensing or Raman spectrometry, have not yet led to stable results. In this review, the main methods for early plant disease detection are discussed. The best proven existing techniques for data acquisition are described. It is discussed how they can be applied to new areas of knowledge. The role of metabolomic approaches in the application of modern methods for early plant disease detection and diagnosis is reviewed. A further direction for experimental methodological development is indicated. The ways to increase the efficiency of modern early plant disease detection remote sensing methods through metabolomic data usage are shown. This article provides an overview of modern sensors and technologies for assessing the biochemical state of crops as well as the ways to apply them in synergy with existing data acquisition and analysis technologies for early plant disease detection.
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Affiliation(s)
- Anton Terentev
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia
| | - Viktor Dolzhenko
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia
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18
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Iruegas-Bocardo F, Weisberg AJ, Riutta ER, Kilday K, Bonkowski JC, Creswell T, Daughtrey ML, Rane K, Grünwald NJ, Chang JH, Putnam ML. Whole Genome Sequencing-Based Tracing of a 2022 Introduction and Outbreak of Xanthomonas hortorum pv. pelargonii. PHYTOPATHOLOGY 2023; 113:975-984. [PMID: 36515656 DOI: 10.1094/phyto-09-22-0321-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Globalization has made agricultural commodities more accessible, available, and affordable. However, their global movement increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. Here, we used 35 strains, isolated by multiple diagnostic laboratories, as a case study for using whole genome sequence data in a plant disease diagnostic setting. Twenty-seven of the strains were isolated in 2022 and identified as Xanthomonas hortorum pv. pelargonii. Eighteen of these strains originated from material sold by a plant breeding company that had notified clients following a release of infected geranium cuttings. Analyses of whole genome sequences revealed epidemiological links among the 27 strains from different growers that confirmed a common source of the outbreak and uncovered likely secondary spread events within facilities that housed plants originating from different plant breeding companies. Whole genome sequencing data were also analyzed to reveal how preparatory and analytical methods can impact conclusions on outbreaks of clonal pathogenic strains. The results demonstrate the potential power of using whole genome sequencing among a network of diagnostic labs and highlight how sharing such data can help shorten response times to mitigate outbreaks more expediently and precisely than standard methods.
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Affiliation(s)
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Elizabeth R Riutta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Kameron Kilday
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - John C Bonkowski
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Tom Creswell
- Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Margery L Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, NY 11901
| | - Karen Rane
- Department of Entomology, University of Maryland, College Park, MD 20742
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97331
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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20
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Singewar K, Fladung M. Double-stranded RNA (dsRNA) technology to control forest insect pests and fungal pathogens: challenges and opportunities. Funct Integr Genomics 2023; 23:185. [PMID: 37243792 DOI: 10.1007/s10142-023-01107-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023]
Abstract
Climate change alters the seasonal synchronization between plants and respective pests plus pathogens. The geographical infiltration helps to shift their hosts, resulting in novel outbreaks that damage forests and ecology. Traditional management schemes are unable to control such outbreaks, therefore unconventional and competitive governance is needed to manage forest pests and pathogens. RNA interference (RNAi) mediated double-stranded RNA (dsRNA) treatment method can be implemented to protect forest trees. Exogenous dsRNA triggers the RNAi-mediated gene silencing of a vital gene, and suspends protein production, resulting in the death of targeted pathogens and pests. The dsRNA treatment method is successful for many crop insects and fungi, however, studies of dsRNA against forest pests and pathogens are depleting. Pesticides and fungicides based on dsRNA could be used to combat pathogens that caused outbreaks in different parts of the world. Although the dsRNA has proved its potential, the crucial dilemma and risks including species-specific gene selection, and dsRNA delivery methods cannot be overlooked. Here, we summarized the major fungi pathogens and insect pests that have caused outbreaks, their genomic information, and studies on dsRNA fungi-and pesticides. Current challenges and opportunities in dsRNA target decision, delivery using nanoparticles, direct applications, and a new method using mycorrhiza for forest tree protection are discussed. The importance of affordable next-generation sequencing to minimize the impact on non-target species is discussed. We suggest that collaborative research among forest genomics and pathology institutes could develop necessary dsRNA strategies to protect forest tree species.
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Affiliation(s)
- Kiran Singewar
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
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21
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Wang X, Qin Y, Xu Y, Feng X, Zhao S, Lu Y, Li Z. Surveillance and invasive risk of the red imported fire ant, Solenopsis invicta Buren in China. PEST MANAGEMENT SCIENCE 2023; 79:1342-1351. [PMID: 36412239 DOI: 10.1002/ps.7297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The red imported fire ant, Solenopsis invicta Buren is one of the world's most successful and destructive invasive ant species. In mainland China, fast, monthly and annual pest reports on all pests have been established since 2010. The distribution of S. invicta resulting from climate change in China was predicted using MaxEnt modeling in combination with comprehensive surveillance data and 56 environmental factors. RESULTS The fast and monthly reports revealed that S. invicta had spread to new territories almost every year in this timeframe. The transportation of seedlings and deployment of turfgrass were the major artificial transmission pathways. Annual reports indicated that control efforts had effectively reduced its occurrence areas and degree of severity of infestations, and retrieved the economic loss caused by S. invicta. The MaxEnt model predicted that S. invicta would expand to 23 provinces in China as a result of climate change. Moisture variables were the key factors affecting the distribution of this pest. CONCLUSION Based on the theoretical reference framework of this research, China proposed the first-ever integrated tactics against a single pest, jointly involving nine ministries, which include clarifying responsibilities, cutting off transmission pathways, strengthening surveillance, declaring pest distributions and conducting preventive and control campaigns. Practical efforts and measures combating the devastation of S. invicta may shed light on its management and other invasive species worldwide. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiaoliang Wang
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
- National Agro-tech Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Yujia Qin
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Yanling Xu
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Xiaodong Feng
- National Agro-tech Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Shouqi Zhao
- National Agro-tech Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Yongyue Lu
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
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22
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Alcalá Briseño RI, Batuman O, Brawner J, Cuellar WJ, Delaquis E, Etherton BA, French-Monar RD, Kreuze JF, Navarrete I, Ogero K, Plex Sulá AI, Yilmaz S, Garrett KA. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1056603. [PMID: 36998684 PMCID: PMC10043385 DOI: 10.3389/fpls.2023.1056603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally.
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Affiliation(s)
- Ricardo I. Alcalá Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Plant Pathology Department, Oregon State University, Corvallis, OR, United States
| | - Ozgur Batuman
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Jeremy Brawner
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Wilmer J. Cuellar
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Erik Delaquis
- International Center for Tropical Agriculture (CIAT), Vientiane, Laos
| | - Berea A. Etherton
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | | | - Jan F. Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru
| | - Israel Navarrete
- Crop and System Sciences Division, International Potato Center (CIP), Quito, Ecuador
| | - Kwame Ogero
- Crop and System Sciences Division, International Potato Center (CIP), Mwanza, Tanzania
| | - Aaron I. Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Salih Yilmaz
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Karen A. Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
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23
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Rossi JP, Rasplus JY. Climate change and the potential distribution of the glassy-winged sharpshooter (Homalodisca vitripennis), an insect vector of Xylella fastidiosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160375. [PMID: 36423847 DOI: 10.1016/j.scitotenv.2022.160375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Biological invasions represent a major threat for biodiversity and agriculture. Despite efforts to restrict the spread of alien species, preventing their introduction remains the best strategy for an efficient control. In that context preparedness of phytosanitary authorities is very important and estimating the geographical range of alien species becomes a key information. The present study investigates the potential geographical range of the glassy-winged sharpshooter (Homalodisca vitripennis), a very efficient insect vector of Xylella fastidiosa, one of the most dangerous plant-pathogenic bacteria worldwide. We use species distribution modeling (SDM) to analyse the climate factors driving the insect distribution and we evaluate its potential distribution in its native range (USA) and in Europe according to current climate and different scenarios of climate change: 6 General Circulation Models (GCM), 4 shared socioeconomic pathways of gas emission and 4 time periods (2030, 2050, 2070, 2090). The first result is that the climate conditions of the European continent are suitable to the glassy-winged sharpshooter, in particular around the Mediterranean basin where X. fastidiosa is present. Projections according to future climate conditions indicate displacement of climatically suitable areas towards the north in both North America and Europe. Globally, suitable areas will decrease in North America and increase in Europe in the coming decades. SDM outputs vary according to the GCM considered and this variability indicated areas of uncertainty in the species potential range. Both potential distribution and its uncertainty associated to future climate projections are important information for improved preparedness of phytosanitary authorities.
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Affiliation(s)
- Jean-Pierre Rossi
- CBGP (Centre de Biologie pour la Gestion des Populations), INRAE, CIRAD, IRD, Institut Agro, Montpellier, France.
| | - Jean-Yves Rasplus
- CBGP (Centre de Biologie pour la Gestion des Populations), INRAE, CIRAD, IRD, Institut Agro, Montpellier, France.
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Zhang W, Sun X, Zhou L, Xie X, Zhao W, Liang Z, Zhuang P. Dual-branch collaborative learning network for crop disease identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1117478. [PMID: 36844059 PMCID: PMC9950499 DOI: 10.3389/fpls.2023.1117478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Crop diseases seriously affect the quality, yield, and food security of crops. redBesides, traditional manual monitoring methods can no longer meet intelligent agriculture's efficiency and accuracy requirements. Recently, deep learning methods have been rapidly developed in computer vision. To cope with these issues, we propose a dual-branch collaborative learning network for crop disease identification, called DBCLNet. Concretely, we propose a dual-branch collaborative module using convolutional kernels of different scales to extract global and local features of images, which can effectively utilize both global and local features. Meanwhile, we embed a channel attention mechanism in each branch module to refine the global and local features. Whereafter, we cascade multiple dual-branch collaborative modules to design a feature cascade module, which further learns features at more abstract levels via the multi-layer cascade design strategy. Extensive experiments on the Plant Village dataset demonstrated the best classification performance of our DBCLNet method compared to the state-of-the-art methods for the identification of 38 categories of crop diseases. Besides, the Accuracy, Precision, Recall, and F-score of our DBCLNet for the identification of 38 categories of crop diseases are 99.89%, 99.97%, 99.67%, and 99.79%, respectively. 811.
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Affiliation(s)
- Weidong Zhang
- School of Information Engineering, Henan Institute of Science and Technology, Xinxiang, China
| | - Xuewei Sun
- School of Information Engineering, Henan Institute of Science and Technology, Xinxiang, China
| | - Ling Zhou
- School of Information Engineering, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiwang Xie
- School of Information Science and Technology, Dalian Maritime University, Dalian, Liaoning, China
| | - Wenyi Zhao
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications (BUPT), Beijing, China
| | - Zheng Liang
- Internet Academy, Anhui University, Hefei, Anhui, China
| | - Peixian Zhuang
- School of Information Engineering, Henan Institute of Science and Technology, Xinxiang, China
- School of Automation and Electrical Engineering, University of Science and Technology Beijing, Beijing, China
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25
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Hovmøller MS, Thach T, Justesen AF. Global dispersal and diversity of rust fungi in the context of plant health. Curr Opin Microbiol 2023; 71:102243. [PMID: 36462410 DOI: 10.1016/j.mib.2022.102243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022]
Abstract
Long-distance dispersal of plant pathogens at the continental scale may have strong implications on plant health, in particular when incursions result in spread of disease to new territories where the disease was previously absent or insignificant. These dispersions may be caused by airborne transmission of spores or accidental spread via human travel and trade. Recent surveillance efforts of cereal rust fungi have demonstrated that incursion of new strains with superior fitness into areas where the disease is already established may have similar implications on plant health. Since dispersal events are highly stochastic, irrespective of transmission mechanism, critical mitigation efforts include preparedness by coordinated pathogen surveillance activities, host crop diversification, and breeding for disease resistance with low vulnerability to sudden changes in the pathogen population.
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Affiliation(s)
- Mogens S Hovmøller
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark.
| | - Tine Thach
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Annemarie F Justesen
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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26
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Giménez-Romero A, Galván J, Montesinos M, Bauzà J, Godefroid M, Fereres A, Ramasco JJ, Matías MA, Moralejo E. Global predictions for the risk of establishment of Pierce's disease of grapevines. Commun Biol 2022; 5:1389. [PMID: 36539523 PMCID: PMC9768138 DOI: 10.1038/s42003-022-04358-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
The vector-borne bacterium Xylella fastidiosa is responsible for Pierce's disease (PD), a lethal grapevine disease that originated in the Americas. The international plant trade is expanding the geographic range of this pathogen, posing a new threat to viticulture worldwide. To assess the potential incidence of PD, we have built a dynamic epidemiological model based on the response of 36 grapevine varieties to the pathogen in inoculation assays and on the vectors' distribution when this information is available. Key temperature-driven epidemiological processes, such as PD symptom development and recovery, are mechanistically modelled. Integrating into the model high-resolution spatiotemporal climatic data from 1981 onward and different infectivity (R0) scenarios, we show how the main wine-producing areas thrive mostly in non-risk, transient, or epidemic-risk zones with potentially low growth rates in PD incidence. Epidemic-risk zones with moderate to high growth rates are currently marginal outside the US. However, a global expansion of epidemic-risk zones coupled with small increments in the disease growth rate is projected for 2050. Our study globally downscales the risk of PD establishment while highlighting the importance of considering climate variability, vector distribution, and an invasive criterion as factors to obtain better PD risk maps.
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Affiliation(s)
- Alex Giménez-Romero
- grid.507629.f0000 0004 1768 3290Instituto de Física Interdisciplinar y Sistemas Complejos, (IFISC-UIB-CSIC), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Javier Galván
- grid.507629.f0000 0004 1768 3290Instituto de Física Interdisciplinar y Sistemas Complejos, (IFISC-UIB-CSIC), Campus UIB, 07122 Palma de Mallorca, Spain
| | | | - Joan Bauzà
- grid.9563.90000 0001 1940 4767Departamento de Geografía, Universidad de las Islas Baleares, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Martin Godefroid
- grid.4711.30000 0001 2183 4846Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, ICA-CSIC, 28006 Madrid, Spain
| | - Alberto Fereres
- grid.4711.30000 0001 2183 4846Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, ICA-CSIC, 28006 Madrid, Spain
| | - José J. Ramasco
- grid.507629.f0000 0004 1768 3290Instituto de Física Interdisciplinar y Sistemas Complejos, (IFISC-UIB-CSIC), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Manuel A. Matías
- grid.507629.f0000 0004 1768 3290Instituto de Física Interdisciplinar y Sistemas Complejos, (IFISC-UIB-CSIC), Campus UIB, 07122 Palma de Mallorca, Spain
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Poggi S, Desneux N, Jactel H, Tayeh C, Verheggen F. A nationwide pest risk analysis in the context of the ongoing Japanese beetle invasion in Continental Europe: The case of metropolitan France. FRONTIERS IN INSECT SCIENCE 2022; 2:1079756. [PMID: 38468800 PMCID: PMC10926453 DOI: 10.3389/finsc.2022.1079756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/25/2022] [Indexed: 03/13/2024]
Abstract
The Japanese beetle, Popillia japonica, is native to Japan and became established in North America in the early twentieth century. The beetle was detected in Europe, first in Italy in 2014 and then in Switzerland in 2017. Metropolitan France is at the forefront of the Japanese beetle threat, due to its geographical proximity to the European populations established in the Piedmont, Lombardy and Ticino regions. An express pest risk analysis for metropolitan France was therefore conducted. The most likely pathways for entry include (i) natural dispersion, (ii) trades of plant products with adherent soil and (iii) hitchhiking behaviour, leading to a high probability of entry. The spread rate of P. japonica was also evaluated as high, resulting from natural spread as well as human activities. Given the absence of significant limiting factors, the potential impacts of P. japonica in France will likely be as important as in its current geographic distribution. Although several sources of uncertainty were highlighted throughout the evaluation, none of them has significant impact on the conclusions of the present express pest risk analysis. Measures to prevent entry, establishment and spread of P. japonica are recommended and include surveillance with pheromone traps and control via integrated pest management strategies. However, most efforts should be concentrated on eradication measures while P. japonica is still in the early stages of invasion.
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Affiliation(s)
- Sylvain Poggi
- IGEPP, Institut Agro, Univ Rennes, INRAE, Le Rheu, France
| | - Nicolas Desneux
- University of Côte d’Azur, INRAE, CNRS, UMR ISA, Nice, France
| | - Hervé Jactel
- INRAE, University of Bordeaux, UMR Biogeco, Cestas, France
| | - Christine Tayeh
- Expertise and Biological Risks Unit (ERB), Plant Health Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Angers, France
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Garrett KA, Bebber DP, Etherton BA, Gold KM, Plex Sulá AI, Selvaraj MG. Climate Change Effects on Pathogen Emergence: Artificial Intelligence to Translate Big Data for Mitigation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:357-378. [PMID: 35650670 DOI: 10.1146/annurev-phyto-021021-042636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant pathology has developed a wide range of concepts and tools for improving plant disease management, including models for understanding and responding to new risks from climate change. Most of these tools can be improved using new advances in artificial intelligence (AI), such as machine learning to integrate massive data sets in predictive models. There is the potential to develop automated analyses of risk that alert decision-makers, from farm managers to national plant protection organizations, to the likely need for action and provide decision support for targeting responses. We review machine-learning applications in plant pathology and synthesize ideas for the next steps to make the most of these tools in digital agriculture. Global projects, such as the proposed global surveillance system for plant disease, will be strengthened by the integration of the wide range of new data, including data from tools like remote sensors, that are used to evaluate the risk ofplant disease. There is exciting potential for the use of AI to strengthen global capacity building as well, from image analysis for disease diagnostics and associated management recommendations on farmers' phones to future training methodologies for plant pathologists that are customized in real-time for management needs in response to the current risks. International cooperation in integrating data and models will help develop the most effective responses to new challenges from climate change.
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Affiliation(s)
- K A Garrett
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - D P Bebber
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - B A Etherton
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - K M Gold
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, New York, USA
| | - A I Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - M G Selvaraj
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Abstract
AbstractThis review addresses ways to prepare for and to mitigate effects of biohazards on primary production of crops and livestock. These biohazards can be natural or intentional introductions of pathogens, and they can cause major economic damage to farmers, the agricultural industry, society, and international trade. Agroterrorism is the intentional introduction of animal or plant pathogens into agricultural production systems with the intention to cause socioeconomic harm and generate public fear. Although few acts of agroterrorism are reported, the threat of agroterrorism in Europe is real. New concerns about threats arise from the rapid advancements in biotechnology and emerging technologies. FORSA, an analytical framework for risk and vulnerability analysis, was used to review how to prepare for and mitigate the possible effects of natural or intentional biohazards in agricultural production. Analyzing the effects of a biohazard event involves multiple scientific disciplines. A comprehensive analysis of biohazards therefore requires a systems approach. The preparedness and ability to manage events are strengthened by bolstered farm biosecurity, increased monitoring and laboratory capacity, improved inter-agency communication and resource allocation. The focus of this review is on Europe, but the insights gained have worldwide applications. The analytical framework used here is compared to other frameworks. With climate change, Covid-19 and the war in Ukraine, the supply chains are challenged, and we foresee increasing food prices associated with social tensions. Our food supply chain becomes more fragile with more unknowns, thereby increasing the needs for risk and vulnerability analyses, of which FORSA is one example.
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Prasanna BM, Carvajal-Yepes M, Kumar PL, Kawarazuka N, Liu Y, Mulema AA, McCutcheon S, Ibabao X. Sustainable management of transboundary pests requires holistic and inclusive solutions. Food Secur 2022. [DOI: 10.1007/s12571-022-01301-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractGlobalization and changing climates are aggravating the occurrence and impacts of transboundary pests, and driving the emergence of new threats. Most of the low- and middle-income countries in Africa, Asia and Latin America are not fully prepared in terms of surveillance, diagnostics, and deployment of plant health solutions due to several factors: adequate investment is lacking; knowledge is inadequate; and connections from the local to global, and global to local are insufficient. Effectively countering the current and emerging threats to plant health requires a holistic approach that includes: 1) globally coordinated diagnostic and surveillance systems; 2) epidemiological modelling, risk assessment, forecasting and preparedness for proactive management and containment; and 3) implementation of context-sensitive, eco-friendly, gender-responsive and socially inclusive integrated disease and pest management approaches to reduce the impacts of devastating transboundary pests and diseases. Despite several success stories where major pests and diseases have been brought to control through integrated approaches, further multi-institutional and multi-disciplinary efforts are necessary. Plant health management requires stronger interface between the biophysical and social sciences, and empowerment of local communities. These reflections derive from the proceedings of a webinar on “Transboundary Disease and Pest Management,” organized by CGIAR (Consultative Group on International Agricultural Research) on March 3, 2021, in recognition of the United Nations designated International Year of Plant Health.
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31
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Alonso Chavez V, Milne AE, van den Bosch F, Pita J, McQuaid CF. Modelling cassava production and pest management under biotic and abiotic constraints. PLANT MOLECULAR BIOLOGY 2022; 109:325-349. [PMID: 34313932 PMCID: PMC9163018 DOI: 10.1007/s11103-021-01170-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
We summarise modelling studies of the most economically important cassava diseases and arthropods, highlighting research gaps where modelling can contribute to the better management of these in the areas of surveillance, control, and host-pest dynamics understanding the effects of climate change and future challenges in modelling. For over 30 years, experimental and theoretical studies have sought to better understand the epidemiology of cassava diseases and arthropods that affect production and lead to considerable yield loss, to detect and control them more effectively. In this review, we consider the contribution of modelling studies to that understanding. We summarise studies of the most economically important cassava pests, including cassava mosaic disease, cassava brown streak disease, the cassava mealybug, and the cassava green mite. We focus on conceptual models of system dynamics rather than statistical methods. Through our analysis we identified areas where modelling has contributed and areas where modelling can improve and further contribute. Firstly, we identify research challenges in the modelling developed for the surveillance, detection and control of cassava pests, and propose approaches to overcome these. We then look at the contributions that modelling has accomplished in the understanding of the interaction and dynamics of cassava and its' pests, highlighting success stories and areas where improvement is needed. Thirdly, we look at the possibility that novel modelling applications can achieve to provide insights into the impacts and uncertainties of climate change. Finally, we identify research gaps, challenges, and opportunities where modelling can develop and contribute for the management of cassava pests, highlighting the recent advances in understanding molecular mechanisms of plant defence.
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Affiliation(s)
- Vasthi Alonso Chavez
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK.
| | - Alice E Milne
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Frank van den Bosch
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Justin Pita
- Laboratory of Plant Physiology, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - C Finn McQuaid
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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32
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Bussell EH, Cunniffe NJ. Optimal strategies to protect a sub-population at risk due to an established epidemic. J R Soc Interface 2022; 19:20210718. [PMID: 35016554 PMCID: PMC8753150 DOI: 10.1098/rsif.2021.0718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epidemics can particularly threaten certain sub-populations. For example, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the elderly are often preferentially protected. For diseases of plants and animals, certain sub-populations can drive mitigation because they are intrinsically more valuable for ecological, economic, socio-cultural or political reasons. Here, we use optimal control theory to identify strategies to optimally protect a ‘high-value’ sub-population when there is a limited budget and epidemiological uncertainty. We use protection of the Redwood National Park in California in the face of the large ongoing state-wide epidemic of sudden oak death (caused by Phytophthora ramorum) as a case study. We concentrate on whether control should be focused entirely within the National Park itself, or whether treatment of the growing epidemic in the surrounding ‘buffer region’ can instead be more profitable. We find that, depending on rates of infection and the size of the ongoing epidemic, focusing control on the high-value region is often optimal. However, priority should sometimes switch from the buffer region to the high-value region only as the local outbreak grows. We characterize how the timing of any switch depends on epidemiological and logistic parameters, and test robustness to systematic misspecification of these factors due to imperfect prior knowledge.
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Affiliation(s)
- Elliott H Bussell
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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33
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Abstract
Plant disease threatens the environmental and financial sustainability of crop production, causing $220 billion in annual losses. The dire threat disease poses to modern agriculture demands tools for better detection and monitoring to prevent crop loss and input waste. The nascent discipline of plant disease sensing, or the science of using proximal and/or remote sensing to detect and diagnose disease, offers great promise to extend monitoring to previously unachievable resolutions, a basis to construct multiscale surveillance networks for early warning, alert, and response at low latency, an opportunity to mitigate loss while optimizing protection, and a dynamic new dimension to agricultural systems biology. Despite its revolutionary potential, plant disease sensing remains an underdeveloped discipline, with challenges facing both fundamental study and field application. This article offers a perspective on the current state and future of plant disease sensing, highlights remaining gaps to be filled, and presents a bold vision for the future of global agriculture.
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Ge T, Jiang H, Tan EH, Johnson SB, Larkin RP, Charkowski AO, Secor G, Hao J. Pangenomic Analysis of Dickeya dianthicola Strains Related to the Outbreak of Blackleg and Soft Rot of Potato in the United States. PLANT DISEASE 2021; 105:3946-3955. [PMID: 34213964 DOI: 10.1094/pdis-03-21-0587-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.
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Affiliation(s)
- Tongling Ge
- School of Food and Agriculture, University of Maine, Orono, ME 04469
| | - He Jiang
- School of Food and Agriculture, University of Maine, Orono, ME 04469
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, ME 04469
| | | | - Robert P Larkin
- USDA-ARS, New England Plant, Soil, and Water Laboratory, University of Maine, Orono, ME 04469
| | - Amy O Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | - Gary Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND58108
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469
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35
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Barro M, Kassankogno AI, Wonni I, Sérémé D, Somda I, Kaboré HK, Béna G, Brugidou C, Tharreau D, Tollenaere C. Spatiotemporal Survey of Multiple Rice Diseases in Irrigated Areas Compared to Rainfed Lowlands in the Western Burkina Faso. PLANT DISEASE 2021; 105:3889-3899. [PMID: 34142847 DOI: 10.1094/pdis-03-21-0579-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Multiple constraints affect rice yields in West Africa. Among these constraints are viral, bacterial, and fungal pathogens. We aimed to describe the spatiotemporal patterns of occurrence and incidence of multiple rice diseases in farmers' fields in contrasting rice growing systems in the western Burkina Faso. For this purpose, we selected a set of three pairs of sites, each comprising an irrigated area and a neighboring rainfed lowland, and studied them over four consecutive years. We first performed interviews with the rice farmers to better characterize the management practices at the different sites. This study revealed that the transplanting of rice and the possibility of growing rice twice a year are restricted to irrigated areas, while other practices, such as the use of registered rice cultivars, fertilization, and pesticides, are not specific but differ between the two rice growing systems. Then, we performed symptom observations at these study sites to monitor the following four diseases: yellow mottle disease, Bacterial Leaf Streak (BLS), rice leaf blast, and brown spot. The infection rates were found to be higher in irrigated areas than in rainfed lowlands, both when analyzing all observed symptoms together (any of the four diseases) and when specifically considering each of the two diseases: BLS and rice leaf blast. Brown spot was particularly prevalent in all six study sites, while yellow mottle disease was particularly structured geographically. Various diseases were frequently found together in the same field (co-occurrence) or even on the same plant (coinfection), especially in irrigated areas.
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Affiliation(s)
- Mariam Barro
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- Université Nazi Boni, Institut du Développement Rural, Laboratoire des Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Irénée Somda
- Université Nazi Boni, Institut du Développement Rural, Laboratoire des Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Hilaire Kouka Kaboré
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PHIM, 34390 Montpellier, France
| | - Gilles Béna
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PHIM, 34390 Montpellier, France
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
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36
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Tagele SB, Kim RH, Shin JH. Interactions between Brassica Biofumigants and Soil Microbiota: Causes and Impacts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11538-11553. [PMID: 34551253 DOI: 10.1021/acs.jafc.1c03776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biofumigation is used to control soil-borne plant diseases, and it has paramount importance to reduce the cost of chemical fumigants. Information about the field control efficacies and impacts of Brassica-based biofumigation (BBF) on soil bacterial and fungal microbiota is scattered in the literature. Therefore, this review summarizes and discusses the nature and the underlying causes of soil bacterial and fungal community dynamics in response to BBF. In addition, the major factors influencing the interaction between a biofumigant and soil microbiota are discussed. The pros and cons of BBF to soil microbiota and the subsequent impacts on sustainable farming practices are also highlighted.
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Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
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37
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Fu P, Jaiswal D, McGrath JM, Wang S, Long SP, Bernacchi CJ. Drought imprints on crops can reduce yield loss: Nature's insights for food security. Food Energy Secur 2021; 11:e332. [PMID: 35846892 PMCID: PMC9285083 DOI: 10.1002/fes3.332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 11/12/2022] Open
Abstract
The Midwestern “Corn‐Belt” in the United States is the most productive agricultural region on the planet despite being predominantly rainfed. In this region, global climate change is driving precipitation patterns toward wetter springs and drier mid‐ to late‐summers, a trend that is likely to intensify in the future. The lack of precipitation can lead to crop water limitations that ultimately impact growth and yields. Young plants exposed to water stress will often invest more resources into their root systems, possibly priming the crop for any subsequent mid‐ or late‐season drought. The trend toward wetter springs, however, suggests that opportunities for crop priming may lessen in the future. Here, we test the hypothesis that early season dry conditions lead to drought priming in field‐grown crops and this response will protect crops against growth and yield losses from late‐season droughts. This hypothesis was tested for the two major Midwestern crop, maize and soybean, using high‐resolution daily weather data, satellite‐derived phenological metrics, field yield data, and ecosystem‐scale model (Agricultural Production System Simulator) simulations. The results from this study showed that priming mitigated yield losses from a late season drought of up to 4.0% and 7.0% for maize and soybean compared with unprimed crops experiencing a late season drought. These results suggest that if the trend toward wet springs with drier summers continues, the relative impact of droughts on crop productivity is likely to worsen. Alternatively, identifying opportunities to breed or genetically modify pre‐primed crop species may provide improved resilience to future climate change.
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Affiliation(s)
- Peng Fu
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Plant Biology and Crop Sciences University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Deepak Jaiswal
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Justin M. McGrath
- USDA‐ARS Global Change and Photosynthesis Research Unit University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Shaowen Wang
- Department of Geography and Geographic Information Science University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Stephen P. Long
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Plant Biology and Crop Sciences University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Carl J. Bernacchi
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Plant Biology and Crop Sciences University of Illinois at Urbana‐Champaign Urbana Illinois USA
- USDA‐ARS Global Change and Photosynthesis Research Unit University of Illinois at Urbana‐Champaign Urbana Illinois USA
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38
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Weisberg AJ, Grünwald NJ, Savory EA, Putnam ML, Chang JH. Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:311-332. [PMID: 34030448 DOI: 10.1146/annurev-phyto-020620-121736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Diseases have a significant cost to agriculture. Findings from analyses of whole-genome sequences show great promise for informing strategies to mitigate risks from diseases caused by phytopathogens. Genomic approaches can be used to dramatically shorten response times to outbreaks and inform disease management in novel ways. However, the use of these approaches requires expertise in working with big, complex data sets and an understanding of their pitfalls and limitations to infer well-supported conclusions. We suggest using an evolutionary framework to guide the use of genomic approaches in epidemiology and diagnostics of plant pathogens. We also describe steps that are necessary for realizing these as standard approaches in disease surveillance.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97331, USA
| | | | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
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39
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de Sousa K, van Etten J, Poland J, Fadda C, Jannink JL, Kidane YG, Lakew BF, Mengistu DK, Pè ME, Solberg SØ, Dell'Acqua M. Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment. Commun Biol 2021; 4:944. [PMID: 34413464 PMCID: PMC8376984 DOI: 10.1038/s42003-021-02463-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Crop breeding must embrace the broad diversity of smallholder agricultural systems to ensure food security to the hundreds of millions of people living in challenging production environments. This need can be addressed by combining genomics, farmers' knowledge, and environmental analysis into a data-driven decentralized approach (3D-breeding). We tested this idea as a proof-of-concept by comparing a durum wheat (Triticum durum Desf.) decentralized trial distributed as incomplete blocks in 1,165 farmer-managed fields across the Ethiopian highlands with a benchmark representing genomic prediction applied to conventional breeding. We found that 3D-breeding could double the prediction accuracy of the benchmark. 3D-breeding could identify genotypes with enhanced local adaptation providing superior productive performance across seasons. We propose this decentralized approach to leverage the diversity in farmer fields and complement conventional plant breeding to enhance local adaptation in challenging crop production environments.
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Affiliation(s)
- Kauê de Sousa
- Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
- Digital Inclusion, Bioversity International, Montpellier, France
| | - Jacob van Etten
- Digital Inclusion, Bioversity International, Montpellier, France
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Carlo Fadda
- Biodiversity for Food and Agriculture, Bioversity International, Nairobi, Kenya
| | - Jean-Luc Jannink
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
| | - Yosef Gebrehawaryat Kidane
- Biodiversity for Food and Agriculture, Bioversity International, Nairobi, Kenya
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Basazen Fantahun Lakew
- Biodiversity for Food and Agriculture, Bioversity International, Nairobi, Kenya
- Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
| | - Dejene Kassahun Mengistu
- Biodiversity for Food and Agriculture, Bioversity International, Nairobi, Kenya
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Svein Øivind Solberg
- Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Matteo Dell'Acqua
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection. Viruses 2021; 13:v13081627. [PMID: 34452491 PMCID: PMC8402784 DOI: 10.3390/v13081627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/26/2023] Open
Abstract
Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
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41
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Valdivia-Granda WA. Known and Unknown Transboundary Infectious Diseases as Hybrid Threats. Front Public Health 2021; 9:668062. [PMID: 34336765 PMCID: PMC8316594 DOI: 10.3389/fpubh.2021.668062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenicity, transmissibility, environmental stability, and potential for genetic manipulation make microbes hybrid threats that could blur the distinction between peace and war. These agents can fall below the detection, attribution, and response capabilities of a nation and seriously affect their health, trade, and security. A framework that could enhance horizon scanning regarding the potential risk of microbes used as hybrid threats requires not only accurately discriminating known and unknown pathogens but building novel scenarios to deploy mitigation strategies. This demands the transition of analyst-based biosurveillance tracking a narrow set of pathogens toward an autonomous biosurveillance enterprise capable of processing vast data streams beyond human cognitive capabilities. Autonomous surveillance systems must gather, integrate, analyze, and visualize billions of data points from different and unrelated sources. Machine learning and artificial intelligence algorithms can contextualize capability information for different stakeholders at different levels of resolution: strategic and tactical. This document provides a discussion of the use of microorganisms as hybrid threats and considerations to quantitatively estimate their risk to ensure societal awareness, preparedness, mitigation, and resilience.
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Garrett KA. Impact network analysis and the
ina r
package: Decision support for regional management interventions. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karen A. Garrett
- Plant Pathology Department Food Systems Institute Emerging Pathogens Institute University of Florida Gainesville FL USA
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Hafeez AN, Arora S, Ghosh S, Gilbert D, Bowden RL, Wulff BBH. Creation and judicious application of a wheat resistance gene atlas. MOLECULAR PLANT 2021; 14:1053-1070. [PMID: 33991673 DOI: 10.1016/j.molp.2021.05.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 05/18/2023]
Abstract
Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.
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Affiliation(s)
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - David Gilbert
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert L Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
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van Dijk M, Morley T, Rau ML, Saghai Y. A meta-analysis of projected global food demand and population at risk of hunger for the period 2010-2050. NATURE FOOD 2021; 2:494-501. [PMID: 37117684 DOI: 10.1038/s43016-021-00322-9] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/16/2021] [Indexed: 04/30/2023]
Abstract
Quantified global scenarios and projections are used to assess long-term future global food security under a range of socio-economic and climate change scenarios. Here, we conducted a systematic literature review and meta-analysis to assess the range of future global food security projections to 2050. We reviewed 57 global food security projection and quantitative scenario studies that have been published in the past two decades and discussed the methods, underlying drivers, indicators and projections. Across five representative scenarios that span divergent but plausible socio-economic futures, the total global food demand is expected to increase by 35% to 56% between 2010 and 2050, while population at risk of hunger is expected to change by -91% to +8% over the same period. If climate change is taken into account, the ranges change slightly (+30% to +62% for total food demand and -91% to +30% for population at risk of hunger) but with no statistical differences overall. The results of our review can be used to benchmark new global food security projections and quantitative scenario studies and inform policy analysis and the public debate on the future of food.
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Affiliation(s)
- Michiel van Dijk
- Wageningen Economic Research, the Hague, the Netherlands.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
| | - Tom Morley
- Wageningen Economic Research, the Hague, the Netherlands
| | | | - Yashar Saghai
- University of Twente, Enschede, the Netherlands
- The Millennium Project Global Futures Studies and Research, Washington DC, USA
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45
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Ristaino JB, Anderson PK, Bebber DP, Brauman KA, Cunniffe NJ, Fedoroff NV, Finegold C, Garrett KA, Gilligan CA, Jones CM, Martin MD, MacDonald GK, Neenan P, Records A, Schmale DG, Tateosian L, Wei Q. The persistent threat of emerging plant disease pandemics to global food security. Proc Natl Acad Sci U S A 2021; 118:e2022239118. [PMID: 34021073 PMCID: PMC8201941 DOI: 10.1073/pnas.2022239118] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world. Now a global human pandemic is threatening the health of millions on our planet. A stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages. In order to tackle these grand challenges, a new set of tools that include disease surveillance and improved detection technologies including pathogen sensors and predictive modeling and data analytics are needed to prevent future outbreaks. Herein, we describe an integrated research agenda that could help mitigate future plant disease pandemics.
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Affiliation(s)
- Jean B Ristaino
- Emerging Plant Disease and Global Food Security Cluster, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695;
| | - Pamela K Anderson
- International Potato Center, 1558 Lima, Peru
- Board for International Food and Agricultural Development, United States Agency for International Development, Washington, DC 20523
| | - Daniel P Bebber
- Biosciences, Exeter University, Exeter EX4 4QD, United Kingdom
| | - Kate A Brauman
- Global Water Initiative, Institute on the Environment, University of Minnesota, St. Paul, MN 55108
| | - Nik J Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Nina V Fedoroff
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16801
| | | | - Karen A Garrett
- Institute for Sustainable Food Systems, University of Florida, Gainesville, FL 32611
- Plant Pathology Department, University of Florida, Gainesville, FL 32611
| | - Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Christopher M Jones
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC 27695
| | - Michael D Martin
- Department of Natural History, Norwegian University of Science and Technology University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Graham K MacDonald
- Department of Geography, McGill University, Montreal, QC, Canada H3A 0B9
| | - Patricia Neenan
- Strategic Partnerships, the Americas, CABI, Wallingford OX10 8DE, United Kingdom
| | - Angela Records
- Bureau for Food Security, United States Agency for International Development, Washington, DC 20523
| | - David G Schmale
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Laura Tateosian
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC 27695
| | - Qingshan Wei
- Emerging Plant Disease and Global Food Security Cluster, Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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Streito JC, Chartois M, Pierre É, Dusoulier F, Armand JM, Gaudin J, Rossi JP. Citizen science and niche modeling to track and forecast the expansion of the brown marmorated stinkbug Halyomorpha halys (Stål, 1855). Sci Rep 2021; 11:11421. [PMID: 34075084 PMCID: PMC8169697 DOI: 10.1038/s41598-021-90378-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
Halyomorpha halys (Stål, 1855), the Brown Marmorated StinkBug (BMSB) is a highly successful invasive species native to eastern Asia that managed to spread into North America and Europe in recent decades. We set up a citizen science survey to monitor BMSB expansion in France in 2012 and analyzed the data it yielded between 2012 and 2019 to examine the local expansion of the insect. These data were gathered with occurrences form various sources (GBIF, literature) to calibrate a species niche model and assess potential current BMSB range. We evaluated the potential changes to the BMSB range due to climate change by projecting the model according to 6 global circulation models (GCM) and the shared socio-economic pathways SSP245 in two time periods 2021-2040 and 2041-2060. Citizen science allowed to track BMSB expansion in France and provided information about its phenology and its habitat preferences. The model highlighted the potential for further range expansion in Europe and illustrated the impact of climate change. These results could help managing the current BMSB invasion and the framework of this survey could contribute to a better preparedness of phytosanitary authorities either for the BMSB or other invasive pests.
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Affiliation(s)
| | | | - Éric Pierre
- UMR CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Jonathan Gaudin
- UMR SAVE INRAE Bordeaux Science Agro, ISVV, Bordeaux, France
| | - Jean-Pierre Rossi
- UMR CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Montpellier, France.
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47
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Huang S, Liu S, Zhang Y, Xie Y, Wang X, Jiao H, Wu S, Zeng Q, Wang Q, Singh RP, Bhavani S, Kang Z, Wang C, Han D, Wu J. Genome-Wide Wheat 55K SNP-Based Mapping of Stripe Rust Resistance Loci in Wheat Cultivar Shaannong 33 and Their Alleles Frequencies in Current Chinese Wheat Cultivars and Breeding Lines. PLANT DISEASE 2021; 105:1048-1056. [PMID: 32965178 DOI: 10.1094/pdis-07-20-1516-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wheat cultivar Shaannong 33 (SN33) has remained highly resistant to stripe rust in the field since its release in 2009. To unravel the genetic architecture of stripe rust resistance, seedlings of 161 recombinant inbred lines (RILs) from the cross Avocet S × SN33 were evaluated with two isolates (PST-Lab.1 and PST-Lab.2) of the stripe rust pathogen (Puccinia striiformis f. sp. tritici) in the greenhouse, and the RILs were evaluated in naturally or artificially inoculated field sites during two cropping seasons. The RILs and parents were genotyped with the wheat 55K single-nucleotide polymorphism array. Three genomic regions conferring seedling resistance were mapped on chromosomes 1DS, 2AS, and 3DS, and four consistent quantitative trait loci (QTL) for adult-plant resistance (APR) were detected on 1BL, 2AS, 3DL, and 6BS. The 2AS locus conferring all-stage resistance was identified as the resistant gene Yr17 located on 2NS translocation. The QTL identified on 1BL and 6BS likely correspond to Yr29 and Yr78, respectively. An APR QTL on 3DL explaining 5.8 to 12.2% of the phenotypic variation is likely to be new. Molecular marker detection assays with the 2NS segment (Yr17), Yr29, Yr78, and QYrsn.nwafu-3DL on a panel of 420 current Chinese wheat cultivars and breeding lines indicated that these genes were present in 11.4, 7.6, 14.8, and 7.4% of entries, respectively. The interactions among these genes and QTL were additive, suggesting their potential value in enhancing stripe rust resistance breeding materials as observed in the resistant parent. In addition, we also identified two leaf necrosis genes, Ne1 and Ne2; however, the F1 plants from cross Avocet S × SN33 survived, indicating that SN33 probably has another allele of Ne1 which allows seed to be harvested.
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Affiliation(s)
- Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yibo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Hanxuan Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shushu Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico 56237, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico 56237, Mexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chengshe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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48
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Emerging infectious diseases threatening food security and economies in Africa. GLOBAL FOOD SECURITY 2021. [DOI: 10.1016/j.gfs.2020.100479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Song S, Wang T, Li Y, Hu J, Kan R, Qiu M, Deng Y, Liu P, Zhang L, Dong H, Li C, Yu D, Li X, Yuan D, Yuan L, Li L. A novel strategy for creating a new system of third-generation hybrid rice technology using a cytoplasmic sterility gene and a genic male-sterile gene. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:251-260. [PMID: 32741081 PMCID: PMC7868973 DOI: 10.1111/pbi.13457] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/09/2020] [Accepted: 07/20/2020] [Indexed: 05/27/2023]
Abstract
Heterosis utilization is the most effective way to improve rice yields. The cytoplasmic male-sterility (CMS) and photoperiod/thermosensitive genic male-sterility (PTGMS) systems have been widely used in rice production. However, the rate of resource utilization for the CMS system hybrid rice is low, and the hybrid seed production for the PTGMS system is affected by the environment. The technical limitations of these two breeding methods restrict the rapid development of hybrid rice. The advantages of the genic male-sterility (GMS) rice, such as stable sterility and free combination, can fill the gaps of the first two generations of hybrid rice technology. At present, the third-generation hybrid rice breeding technology is being used to realize the application of GMS materials in hybrid rice. This study aimed to use an artificial CMS gene as a pollen killer to create a smart sterile line for hybrid rice production. The clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) technology was used to successfully obtain a CYP703A3-deficient male-sterile mutant containing no genetically modified component in the genetic background of indica 9311. Through young ear callus transformation, this mutant was transformed with three sets of element-linked expression vectors, including pollen fertility restoration gene CYP703A3, pollen-lethality gene orfH79 and selection marker gene DsRed2. The maintainer 9311-3B with stable inheritance was obtained, which could realize the batch breeding of GMS materials. Further, the sterile line 9311-3A and restorer lines were used for hybridization, and a batch of superior combinations of hybrid rice was obtained.
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Affiliation(s)
- Shufeng Song
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Tiankang Wang
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Yixing Li
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Jun Hu
- State Key Laboratory of Hybrid RiceEngineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life SciencesWuhan UniversityWuhanChina
| | - Ruifeng Kan
- State Key Laboratory of Applied OpticsChangchun Institute of OpticsFine Mechanics & PhysicsChinese Academy of SciencesChangchunChina
| | - Mudan Qiu
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Yingde Deng
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Peixun Liu
- State Key Laboratory of Applied OpticsChangchun Institute of OpticsFine Mechanics & PhysicsChinese Academy of SciencesChangchunChina
| | - Licheng Zhang
- College of AgronomyHunan Agricultural UniversityChangshaChina
| | - Hao Dong
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
- Long Ping BranchGraduate School of Hunan UniversityChangshaChina
| | - Chengxia Li
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Dong Yu
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Xinqi Li
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Dingyang Yuan
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Longping Yuan
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
| | - Li Li
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaChina
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50
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Carlier J, Robert S, Roussel V, Chilin-Charles Y, Lubin-Adjanoh N, Gilabert A, Abadie C. Central American and Caribbean population history of the Pseudocercospora fijiensis fungus responsible for the latest worldwide pandemics on banana. Fungal Genet Biol 2021; 148:103528. [PMID: 33515682 DOI: 10.1016/j.fgb.2021.103528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/18/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Among the emerging fungal diseases threatening food security, the Pseudocercospora fijiensis fungus causing black leaf streak disease of banana is one of the most marked examples of a recent worldwide pandemic on a major crop. We assessed how this pathogen spread throughout the latest invaded region, i.e. Central America and the Caribbean. We retraced its population history combining detailed monitoring information on disease outbreaks and population genetic analyses based on large-scale sampling of P. fijiensis isolates from 121 locations throughout the region. The results first suggested that sexual reproduction was not lost during the P. fijiensis expansion, even in the insular Caribbean context, and a high level of genotypic diversity was maintained in all the populations studied. The population genetic structure of P. fijiensis and historical data showed that two disease waves swept northward and southward in all banana-producing countries in the study area from an initial entry point in Honduras, probably mainly through gradual stepwise spore dispersal. Serial founder events accompanying the northern and southern waves led to the establishment of two different genetic groups. A different population structure was detected on the latest invaded islands (Martinique, Dominica and Guadeloupe), revealing multiple introductions and admixture events that may have been partly due to human activities. The results of this study highlight the need to step up surveillance to limit the spread of other known emerging diseases of banana spread mainly by humans, but also to curb gene flow between established pathogen populations which could increase their evolutionary potential.
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Affiliation(s)
- Jean Carlier
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
| | - Stéphanie Robert
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Véronique Roussel
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Yolande Chilin-Charles
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nadia Lubin-Adjanoh
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Aude Gilabert
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Catherine Abadie
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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