The weight initialization technique for transfer learning refers to the practice of using pretrained models that can be modified to solve new problems, instead of starting the training process from scratch. In this study, six different transfer learning weight initialization strategies were proposed for plant disease detection: scratch (i.e., random initialization), pretrained model on cross‐domain (ImageNet), model trained on related domain (ISIC 2019), model trained on related domain (ISIC 2019) with cross‐domain (ImageNet) weights, model trained on same domain (PlantVillage), and model trained on same domain (PlantVillage) with cross‐domain weights (ImageNet). Weights from each strategy were transferred to a target dataset (Plant Pathology 2021). These strategies were implemented using eight deep learning architectures. It was observed that transferring from any strategy led to an average acceleration of convergence ranging from 33.88% to 73.16% in mean loss and an improvement of 8.72%–42.12% in mean F1‐score compared to the scratch strategy. Moreover, although smaller and less comprehensive than ImageNet, transferring information from the same domain or related domain proved to be competitive compared to transferring from ImageNet. This indicates that ImageNet, which is widely favoured in the literature, may not necessarily represent the most optimal transfer source for the given context. In addition, to identify which strategies have significant differences, a post hoc analysis using Tukey's HSD test was conducted. Finally, the classifications made by the proposed models were visualized using Grad‐CAM to provide a qualitative understanding of how different weight initialization strategies affect the focus areas of the models.
{"title":"Effect of different weight initialization strategies on transfer learning for plant disease detection","authors":"Duygu Sinanc Terzi","doi":"10.1111/ppa.13997","DOIUrl":"https://doi.org/10.1111/ppa.13997","url":null,"abstract":"The weight initialization technique for transfer learning refers to the practice of using pretrained models that can be modified to solve new problems, instead of starting the training process from scratch. In this study, six different transfer learning weight initialization strategies were proposed for plant disease detection: scratch (i.e., random initialization), pretrained model on cross‐domain (ImageNet), model trained on related domain (ISIC 2019), model trained on related domain (ISIC 2019) with cross‐domain (ImageNet) weights, model trained on same domain (PlantVillage), and model trained on same domain (PlantVillage) with cross‐domain weights (ImageNet). Weights from each strategy were transferred to a target dataset (Plant Pathology 2021). These strategies were implemented using eight deep learning architectures. It was observed that transferring from any strategy led to an average acceleration of convergence ranging from 33.88% to 73.16% in mean loss and an improvement of 8.72%–42.12% in mean F<jats:sub>1</jats:sub>‐score compared to the scratch strategy. Moreover, although smaller and less comprehensive than ImageNet, transferring information from the same domain or related domain proved to be competitive compared to transferring from ImageNet. This indicates that ImageNet, which is widely favoured in the literature, may not necessarily represent the most optimal transfer source for the given context. In addition, to identify which strategies have significant differences, a post hoc analysis using Tukey's HSD test was conducted. Finally, the classifications made by the proposed models were visualized using Grad‐CAM to provide a qualitative understanding of how different weight initialization strategies affect the focus areas of the models.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"40 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shriprabha R. Upadhyaya, Monica F. Danilevicz, Aria Dolatabadian, Ting Xiang Neik, Fangning Zhang, Hawlader A. Al‐Mamun, Mohammed Bennamoun, Jacqueline Batley, David Edwards
Plant disease outbreaks continuously challenge food security and sustainability. Traditional chemical methods used to treat diseases have environmental and health concerns, raising the need to enhance inherent plant disease resistance mechanisms. Traits, including disease resistance, can be linked to specific loci in the genome and identifying these markers facilitates targeted breeding approaches. Several methods, including genome‐wide association studies and genomic selection, have been used to identify important markers and select varieties with desirable traits. However, these traditional approaches may not fully capture the non‐linear characteristics of the effect of genomic variation on traits. Machine learning, known for its data‐mining abilities, offers an opportunity to enhance the accuracy of the existing trait association approaches. It has found applications in predicting various agronomic traits across several species. However, its use in disease resistance prediction remains limited. This review highlights the potential of machine learning as a complementary tool for predicting the genetic loci contributing to pathogen resistance. We provide an overview of traditional trait prediction methods, summarize machine‐learning applications, and address the challenges and opportunities associated with machine learning‐based crop disease resistance prediction.
{"title":"Genomics‐based plant disease resistance prediction using machine learning","authors":"Shriprabha R. Upadhyaya, Monica F. Danilevicz, Aria Dolatabadian, Ting Xiang Neik, Fangning Zhang, Hawlader A. Al‐Mamun, Mohammed Bennamoun, Jacqueline Batley, David Edwards","doi":"10.1111/ppa.13988","DOIUrl":"https://doi.org/10.1111/ppa.13988","url":null,"abstract":"Plant disease outbreaks continuously challenge food security and sustainability. Traditional chemical methods used to treat diseases have environmental and health concerns, raising the need to enhance inherent plant disease resistance mechanisms. Traits, including disease resistance, can be linked to specific loci in the genome and identifying these markers facilitates targeted breeding approaches. Several methods, including genome‐wide association studies and genomic selection, have been used to identify important markers and select varieties with desirable traits. However, these traditional approaches may not fully capture the non‐linear characteristics of the effect of genomic variation on traits. Machine learning, known for its data‐mining abilities, offers an opportunity to enhance the accuracy of the existing trait association approaches. It has found applications in predicting various agronomic traits across several species. However, its use in disease resistance prediction remains limited. This review highlights the potential of machine learning as a complementary tool for predicting the genetic loci contributing to pathogen resistance. We provide an overview of traditional trait prediction methods, summarize machine‐learning applications, and address the challenges and opportunities associated with machine learning‐based crop disease resistance prediction.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"16 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ritisha N. Tatmiya, Shital M. Padhiyar, Sangh Chandramohan, Sandip K. Bera, Shradda B. Bhatt, Mir Asif Iquebal, Padma S. Ambalam, Rukam S. Tomar
This study aimed to explore transcriptomic distinctions between resistant (CS‐319) and susceptible (JAL‐42) groundnut (Arachis hypogaea) genotypes exposed to Sclerotium rolfsii infection across different developmental stages. Employing a de novo assembly‐based approach, we analysed the transcriptomic response in these groundnut plants under control and infected conditions at 24, 72 and 120 hours post‐inoculation (hpi). Our RNA‐Seq data yielded a total of 133,900,261 reads, revealing 7796 differentially expressed genes (DEGs). We constructed a gene regulatory network with 59 hub genes, identified 6783 transcription factors and uncovered 88,424 putative markers, including 17,236 simple‐sequence repeats (SSRs), 10,099 single‐nucleotide polymorphisms (SNPs) and 78,332 indels. Notably, the majority of DEGs were upregulated at 24 hpi in the resistant genotype, encompassing diverse functional categories such as pathogenesis‐related genes, defence‐related (R) genes, genes involved in plant–fungus interactions, oxidation–reduction‐related genes, transport, metabolism and proteolysis genes, along with transcription factors (FAR1, B3, GATA, NAC, WRKY, MYBC1 and bHLH), secondary metabolic pathway‐related genes and photosynthesis‐related genes. The up‐regulation of WRKY transcripts, associated with the activation of the jasmonic acid defence signalling pathway, potentially induced systemic acquired resistance (SAR). Conversely, these DEGs exhibited down‐regulation in the susceptible genotype. Furthermore, a total of 17,236 expressed sequence tag (EST)‐SSRs were identified from the unigenes, holding significant potential for advancing plant breeding through marker‐assisted methods, facilitating quantitative trait locus (QTL) mapping and evaluating genetic diversity among genotypes. This study's approach contributes to a more profound understanding of the molecular‐level defence mechanisms involved in the interaction between groundnuts and S. rolfsii.
{"title":"Comparative transcriptome profiling of resistant and susceptible groundnut (Arachis hypogaea) genotypes in response to stem rot infection caused by Sclerotium rolfsii","authors":"Ritisha N. Tatmiya, Shital M. Padhiyar, Sangh Chandramohan, Sandip K. Bera, Shradda B. Bhatt, Mir Asif Iquebal, Padma S. Ambalam, Rukam S. Tomar","doi":"10.1111/ppa.13987","DOIUrl":"https://doi.org/10.1111/ppa.13987","url":null,"abstract":"This study aimed to explore transcriptomic distinctions between resistant (CS‐319) and susceptible (JAL‐42) groundnut (<jats:italic>Arachis hypogaea</jats:italic>) genotypes exposed to <jats:italic>Sclerotium rolfsii</jats:italic> infection across different developmental stages. Employing a de novo assembly‐based approach, we analysed the transcriptomic response in these groundnut plants under control and infected conditions at 24, 72 and 120 hours post‐inoculation (hpi). Our RNA‐Seq data yielded a total of 133,900,261 reads, revealing 7796 differentially expressed genes (DEGs). We constructed a gene regulatory network with 59 hub genes, identified 6783 transcription factors and uncovered 88,424 putative markers, including 17,236 simple‐sequence repeats (SSRs), 10,099 single‐nucleotide polymorphisms (SNPs) and 78,332 indels. Notably, the majority of DEGs were upregulated at 24 hpi in the resistant genotype, encompassing diverse functional categories such as pathogenesis‐related genes, defence‐related (R) genes, genes involved in plant–fungus interactions, oxidation–reduction‐related genes, transport, metabolism and proteolysis genes, along with transcription factors (FAR1, B3, GATA, NAC, WRKY, MYBC1 and bHLH), secondary metabolic pathway‐related genes and photosynthesis‐related genes. The up‐regulation of WRKY transcripts, associated with the activation of the jasmonic acid defence signalling pathway, potentially induced systemic acquired resistance (SAR). Conversely, these DEGs exhibited down‐regulation in the susceptible genotype. Furthermore, a total of 17,236 expressed sequence tag (EST)‐SSRs were identified from the unigenes, holding significant potential for advancing plant breeding through marker‐assisted methods, facilitating quantitative trait locus (QTL) mapping and evaluating genetic diversity among genotypes. This study's approach contributes to a more profound understanding of the molecular‐level defence mechanisms involved in the interaction between groundnuts and <jats:italic>S</jats:italic>. <jats:italic>rolfsii</jats:italic>.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"24 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Reem Aboukhaddour, Brent D. McCallum, Jim Menzies, Colin Hiebert
The cultivation of wheat in North America represents a relatively recent endeavour, spanning a mere 150 years. This relatively brief period of its recent cultivation has allowed the opportunity to document the threats and diseases farmers had to face from the start. In this minireview, our primary objective is to provide a detailed exploration of the historical context on how we end up effectively managing what was once among the most destructive and hard to manage diseases affecting wheat, namely, common bunt (covered smut). This review delves into the early research efforts dedicated to understanding the biology of the causal pathogens and developing effective management approaches. These efforts encompass a wide spectrum of potential methods, ranging from seed treatments to cropping practices, and the development of genetic resistance. Throughout this exploration, we will also spotlight the remarkable scientific success story that has unfolded within the Canadian context. In essence, this review aims to provide a scientific examination of the history, challenges and innovative approaches associated with mitigating the impact of bunt pathogens on wheat cultivation in North America, and future challenges.
{"title":"The scientific journey to eradicate smuts on the prairies","authors":"Reem Aboukhaddour, Brent D. McCallum, Jim Menzies, Colin Hiebert","doi":"10.1111/ppa.13990","DOIUrl":"https://doi.org/10.1111/ppa.13990","url":null,"abstract":"The cultivation of wheat in North America represents a relatively recent endeavour, spanning a mere 150 years. This relatively brief period of its recent cultivation has allowed the opportunity to document the threats and diseases farmers had to face from the start. In this minireview, our primary objective is to provide a detailed exploration of the historical context on how we end up effectively managing what was once among the most destructive and hard to manage diseases affecting wheat, namely, common bunt (covered smut). This review delves into the early research efforts dedicated to understanding the biology of the causal pathogens and developing effective management approaches. These efforts encompass a wide spectrum of potential methods, ranging from seed treatments to cropping practices, and the development of genetic resistance. Throughout this exploration, we will also spotlight the remarkable scientific success story that has unfolded within the Canadian context. In essence, this review aims to provide a scientific examination of the history, challenges and innovative approaches associated with mitigating the impact of bunt pathogens on wheat cultivation in North America, and future challenges.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"22 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Niroshini Gunasinghe, Niloofar Vaghefi, Roger G. Shivas, Yu Pei Tan, David Jordan, Emma Mace, Anke Martin
Stalk and root rots of cultivated sorghum (Sorghum bicolor) are caused by several Fusarium species worldwide. This study evaluated Fusarium diversity, pathogenicity and population structure amongst 212 isolates obtained from 169 sorghum plants from commercial field crops in eastern Australia. Sequences of translation elongation factor‐1α (tef‐1α), RNA polymerase II largest subunit (rpb1), RNA polymerase II second largest subunit (rpb2) and calmodulin (cmdA) were used to construct multilocus phylogenies that enabled the identification of 16 Fusarium species in Fusarium chlamydosporum species complex (FCSC), Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum‐equiseti species complex and Fusarium oxysporum species complex (FOSC). The majority of isolates (n = 171) belonged to FFSC. The pathogenicity of 17 selected isolates was determined by artificial inoculation of sorghum seedlings and completing Koch's postulates. Isolates of species in FFSC were significantly (p < 0.05) more aggressive as root pathogens in sorghum seedlings than isolates of other species tested and widely distributed across all sampling sites. Amongst the 35 isolates of FOSC, 26 belonged to Fusarium cili, which is only known as an endophyte from healthy roots of Rosa roxburghii in China. Fusarium sporodochiale (in FCSC) and Fusarium contaminatum (in FOSC) are reported as sorghum seedling root rot pathogens for the first time.
在全球范围内，栽培高粱（Sorghum bicolor）的茎腐病和根腐病是由多种镰刀菌引起的。本研究评估了从澳大利亚东部 169 株高粱作物中分离的 212 株镰刀菌的多样性、致病性和种群结构。研究人员利用翻译延伸因子-1α（tef-1α）、RNA聚合酶 II 最大亚基（rpb1）、RNA聚合酶 II 第二大亚基（rpb2）和钙调蛋白（cmdA）的序列构建了多聚焦系统进化论，从而确定了衣壳镰刀菌种群（FCSC）中的 16 个镰刀菌种、Fusarium incarnatum-equiseti species complex and Fusarium oxysporum species complex (FOSC)。大多数分离物（n = 171）属于 FFSC。通过对高粱秧苗进行人工接种，并根据科赫定理确定了 17 个所选分离株的致病性。作为高粱幼苗根部的病原体，FFSC 物种的分离物比其他物种的分离物具有更强的侵染性（p < 0.05），并且广泛分布于所有采样点。在 35 个 FOSC 分离物中，有 26 个属于纤毛镰刀菌，而纤毛镰刀菌在中国仅作为内生菌存在于罗布麻的健康根部。高粱苗根腐病病原菌中的孢子镰刀菌（Fusarium sporodochiale，FSC）和污染镰刀菌（Fusarium contaminatum，FOSC）为首次报道。
{"title":"Diversity and pathogenicity of Fusarium spp. isolated from cultivated sorghum stems and roots in eastern Australia","authors":"Niroshini Gunasinghe, Niloofar Vaghefi, Roger G. Shivas, Yu Pei Tan, David Jordan, Emma Mace, Anke Martin","doi":"10.1111/ppa.13985","DOIUrl":"https://doi.org/10.1111/ppa.13985","url":null,"abstract":"Stalk and root rots of cultivated sorghum (<jats:italic>Sorghum bicolor</jats:italic>) are caused by several <jats:italic>Fusarium</jats:italic> species worldwide. This study evaluated <jats:italic>Fusarium</jats:italic> diversity, pathogenicity and population structure amongst 212 isolates obtained from 169 sorghum plants from commercial field crops in eastern Australia. Sequences of translation elongation factor‐1α (<jats:italic>tef‐1α</jats:italic>), RNA polymerase II largest subunit (<jats:italic>rpb1</jats:italic>), RNA polymerase II second largest subunit (<jats:italic>rpb2</jats:italic>) and calmodulin (<jats:italic>cmdA</jats:italic>) were used to construct multilocus phylogenies that enabled the identification of 16 <jats:italic>Fusarium</jats:italic> species in <jats:italic>Fusarium chlamydosporum</jats:italic> species complex (FCSC), <jats:italic>Fusarium fujikuroi</jats:italic> species complex (FFSC), <jats:italic>Fusarium incarnatum‐equiseti</jats:italic> species complex and <jats:italic>Fusarium oxysporum</jats:italic> species complex (FOSC). The majority of isolates (<jats:italic>n</jats:italic> = 171) belonged to FFSC. The pathogenicity of 17 selected isolates was determined by artificial inoculation of sorghum seedlings and completing Koch's postulates. Isolates of species in FFSC were significantly (<jats:italic>p</jats:italic> < 0.05) more aggressive as root pathogens in sorghum seedlings than isolates of other species tested and widely distributed across all sampling sites. Amongst the 35 isolates of FOSC, 26 belonged to <jats:italic>Fusarium cili</jats:italic>, which is only known as an endophyte from healthy roots of <jats:italic>Rosa roxburghii</jats:italic> in China. <jats:italic>Fusarium sporodochiale</jats:italic> (in FCSC) and <jats:italic>Fusarium contaminatum</jats:italic> (in FOSC) are reported as sorghum seedling root rot pathogens for the first time.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"11 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tatiane Paulino da Cruz, Matheus Ricardo da Rocha, Sophia Machado Ferreira da Silva, Willian Bucker Moraes, Simone de Paiva Caetano Bucker Moraes, Poliana Aparecida Rodrigues Gazolla, Mariana Belizário de Oliveira, Vagner Tebaldi de Queiroz, Róbson Ricardo Teixeira, Osmair Vital de Oliveira, Juliana Alves Resende, Adilson Vidal Costa, Waldir Cintra de Jesus Junior
Coffee leaf rust (CLR), caused by Hemileia vastatrix, poses a significant threat to global coffee production, resulting in substantial economic losses. This study explores the effectiveness of triazole derivatives synthesized from glycerol in controlling CLR in conilon coffee (Coffea canephora). In vitro assays evaluated the inhibitory effect of triazole derivatives (4a–4q) at concentrations of 10, 25, 50, 75 and 100 ppm on H. vastatrix urediniospore germination, followed by greenhouse experiments to assess their preventive and curative potential. Preventive and curative sprayings of the four most efficient triazoles were conducted on seedlings inoculated with H. vastatrix at concentrations ranging from 0 to 400 ppm, evaluating severity, sporulation, incubation and latent periods. Triazole derivatives 4b, 4d, 4f and 4o effectively suppressed H. vastatrix urediniospore germination, achieving reductions between 9.9% and 78.8%. In greenhouse trials, these compounds demonstrated preventive efficacy by prolonging incubation and latent periods, reducing sporulation and mitigating rust severity, with triazole 4f exhibiting the highest efficiency. Furthermore, the derivatives showed effectiveness in curative treatments, particularly triazole 4f. Physiological analyses indicated no significant alterations in coffee plant metabolism, suggesting the safety of these compounds for agricultural use. Molecular docking studies elucidated their mechanism of action, suggesting their potential as antifungal agents by interacting with the HvCYP51 enzyme involved in ergosterol biosynthesis. Overall, the study underscores the promising efficacy of glycerol‐derived triazole derivatives in managing CLR, providing sustainable solutions for disease control in agriculture.
{"title":"Fungicidal activity and molecular docking of glycerol‐derived triazole compounds for controlling coffee leaf rust","authors":"Tatiane Paulino da Cruz, Matheus Ricardo da Rocha, Sophia Machado Ferreira da Silva, Willian Bucker Moraes, Simone de Paiva Caetano Bucker Moraes, Poliana Aparecida Rodrigues Gazolla, Mariana Belizário de Oliveira, Vagner Tebaldi de Queiroz, Róbson Ricardo Teixeira, Osmair Vital de Oliveira, Juliana Alves Resende, Adilson Vidal Costa, Waldir Cintra de Jesus Junior","doi":"10.1111/ppa.13986","DOIUrl":"https://doi.org/10.1111/ppa.13986","url":null,"abstract":"Coffee leaf rust (CLR), caused by <jats:italic>Hemileia vastatrix</jats:italic>, poses a significant threat to global coffee production, resulting in substantial economic losses. This study explores the effectiveness of triazole derivatives synthesized from glycerol in controlling CLR in conilon coffee (<jats:italic>Coffea canephora</jats:italic>). In vitro assays evaluated the inhibitory effect of triazole derivatives (4a–4q) at concentrations of 10, 25, 50, 75 and 100 ppm on <jats:italic>H</jats:italic>. <jats:italic>vastatrix</jats:italic> urediniospore germination, followed by greenhouse experiments to assess their preventive and curative potential. Preventive and curative sprayings of the four most efficient triazoles were conducted on seedlings inoculated with <jats:italic>H</jats:italic>. <jats:italic>vastatrix</jats:italic> at concentrations ranging from 0 to 400 ppm, evaluating severity, sporulation, incubation and latent periods. Triazole derivatives 4b, 4d, 4f and 4o effectively suppressed <jats:italic>H</jats:italic>. <jats:italic>vastatrix</jats:italic> urediniospore germination, achieving reductions between 9.9% and 78.8%. In greenhouse trials, these compounds demonstrated preventive efficacy by prolonging incubation and latent periods, reducing sporulation and mitigating rust severity, with triazole 4f exhibiting the highest efficiency. Furthermore, the derivatives showed effectiveness in curative treatments, particularly triazole 4f. Physiological analyses indicated no significant alterations in coffee plant metabolism, suggesting the safety of these compounds for agricultural use. Molecular docking studies elucidated their mechanism of action, suggesting their potential as antifungal agents by interacting with the HvCYP51 enzyme involved in ergosterol biosynthesis. Overall, the study underscores the promising efficacy of glycerol‐derived triazole derivatives in managing CLR, providing sustainable solutions for disease control in agriculture.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"2 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tony Reglinski, Kirstin Wurms, Grant Northcott, Joseph Taylor, Annette Ah Chee, Frank Parry, Christina Fehlmann, Janine Cooney, Dwayne Jensen, Philip Elmer, Stephen Hoyte, Catherine McKenzie, Duncan Hedderley
The artificial sweetener saccharin has been reported to enhance resistance against pathogen attack in various plant species. In this study, foliar application of saccharin resulted in increased resistance to leaf infection by Pseudomonas syringae pv. actinidiae biovar 3 (Psa) in two Actinidia chinensis cultivars, Hayward and Zesy002. In glasshouse plants, the application of saccharin at 0.25, 0.5, 1.0 and 2.0 g/L, 1 week before inoculation with Psa, induced a dose‐dependent reduction in leaf necrosis in both cultivars. Saccharin at 2.0 g/L reduced leaf necrosis in Hayward by 77% and in Zesy002 by over 90%. However, saccharin (2.0 g/L) did not inhibit growth of Psa in liquid media, thus suggesting induced resistance (IR) as the primary mode of action against leaf infection. The development of IR in both cultivars was concomitant with the accumulation of salicylic acid (SA) and salicylate glycoside (SAG), and the upregulation of SA‐pathway genes (PR1 and PR2) in treated leaves. In orchard‐grown Hayward vines, saccharin (1.0 g/L) induced the upregulation of SA‐pathway genes and reduced Psa leaf necrosis and flower bud rot by 50% and 25%, respectively, compared with controls. However, saccharin residues were detected in fruit collected from vines that were sprayed with saccharin (1.0 g/L) before flowering. Residue level correlated with application frequency and timing and was highest (0.051 mg/kg) in vines that received three preflowering sprays. This exceeds the default maximum residue limit (MRL; 0.01 mg/kg) for some export markets and could limit the use of saccharin for disease management.
{"title":"Saccharin induces resistance against Pseudomonas syringae pv. actinidiae (Psa biovar 3) in glasshouse kiwifruit and orchard vines","authors":"Tony Reglinski, Kirstin Wurms, Grant Northcott, Joseph Taylor, Annette Ah Chee, Frank Parry, Christina Fehlmann, Janine Cooney, Dwayne Jensen, Philip Elmer, Stephen Hoyte, Catherine McKenzie, Duncan Hedderley","doi":"10.1111/ppa.13984","DOIUrl":"https://doi.org/10.1111/ppa.13984","url":null,"abstract":"The artificial sweetener saccharin has been reported to enhance resistance against pathogen attack in various plant species. In this study, foliar application of saccharin resulted in increased resistance to leaf infection by <jats:italic>Pseudomonas syringae</jats:italic> pv. <jats:italic>actinidiae</jats:italic> biovar 3 (Psa) in two <jats:italic>Actinidia chinensis</jats:italic> cultivars, Hayward and Zesy002. In glasshouse plants, the application of saccharin at 0.25, 0.5, 1.0 and 2.0 g/L, 1 week before inoculation with Psa, induced a dose‐dependent reduction in leaf necrosis in both cultivars. Saccharin at 2.0 g/L reduced leaf necrosis in Hayward by 77% and in Zesy002 by over 90%. However, saccharin (2.0 g/L) did not inhibit growth of Psa in liquid media, thus suggesting induced resistance (IR) as the primary mode of action against leaf infection. The development of IR in both cultivars was concomitant with the accumulation of salicylic acid (SA) and salicylate glycoside (SAG), and the upregulation of SA‐pathway genes (<jats:italic>PR1</jats:italic> and <jats:italic>PR2</jats:italic>) in treated leaves. In orchard‐grown Hayward vines, saccharin (1.0 g/L) induced the upregulation of SA‐pathway genes and reduced Psa leaf necrosis and flower bud rot by 50% and 25%, respectively, compared with controls. However, saccharin residues were detected in fruit collected from vines that were sprayed with saccharin (1.0 g/L) before flowering. Residue level correlated with application frequency and timing and was highest (0.051 mg/kg) in vines that received three preflowering sprays. This exceeds the default maximum residue limit (MRL; 0.01 mg/kg) for some export markets and could limit the use of saccharin for disease management.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"12 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142183775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Irina Popescu, A. Kiripuvaney Loganathan, Hailey R. Graham, Tyler J. Avis
Anthracnose, caused by Colletotrichum spp., is a threat to strawberry production globally. Unlike their chemical counterparts, microbial biofungicides offer a method of postharvest fungal disease control that is safe, sustainable and less affected by pathogen resistance. The present study evaluated the antifungal effects of three bacteria, Bacillus velezensis strains SH1 and SH2 and Pseudomonas azotoformans strain SH3, obtained from sheep manure compost tea. The bacteria or their cell‐free filtrates were tested against Colletotrichum acutatum and Colletotrichum gloeosporioides in bioassays and against strawberry anthracnose. In addition, precipitated or extracted extracellular fractions were tested to determine the effects on membrane permeability of Colletotrichum spp. spores. Confrontation assay results showed all bacteria inhibited mycelial growth, with B. velezensis SH1 and P. azotoformans SH3 being the most effective. All cell‐free filtrates inhibited mycelial growth with B. velezensis SH1 and SH2 resulting in the highest inhibition. The bacteria suppressed anthracnose lesions on strawberry fruit although effective treatments varied by causal mould. B. velezensis SH1 and SH2 significantly permeabilized spore membranes, indicating antibiosis as a possible mode of action. Investigation into antimicrobial compound production found various homologues of the lipopeptides fengycin, iturin and surfactin were produced by B. velezensis SH1 and SH2. Results suggest that lipopeptides produced by B. velezensis strains permeabilize Colletotrichum cell membranes, and that fengycins were the most inhibitory of the lipopeptides against Colletotrichum spp.
{"title":"Antifungal activity of Bacillus velezensis and Pseudomonas azotoformans isolated from compost tea against anthracnose (Colletotrichum spp.) on strawberry fruit","authors":"Irina Popescu, A. Kiripuvaney Loganathan, Hailey R. Graham, Tyler J. Avis","doi":"10.1111/ppa.13983","DOIUrl":"https://doi.org/10.1111/ppa.13983","url":null,"abstract":"Anthracnose, caused by <jats:italic>Colletotrichum</jats:italic> spp., is a threat to strawberry production globally. Unlike their chemical counterparts, microbial biofungicides offer a method of postharvest fungal disease control that is safe, sustainable and less affected by pathogen resistance. The present study evaluated the antifungal effects of three bacteria, <jats:italic>Bacillus velezensis</jats:italic> strains SH1 and SH2 and <jats:italic>Pseudomonas azotoformans</jats:italic> strain SH3, obtained from sheep manure compost tea. The bacteria or their cell‐free filtrates were tested against <jats:italic>Colletotrichum acutatum</jats:italic> and <jats:italic>Colletotrichum gloeosporioides</jats:italic> in bioassays and against strawberry anthracnose. In addition, precipitated or extracted extracellular fractions were tested to determine the effects on membrane permeability of <jats:italic>Colletotrichum</jats:italic> spp. spores. Confrontation assay results showed all bacteria inhibited mycelial growth, with <jats:italic>B</jats:italic>. <jats:italic>velezensis</jats:italic> SH1 and <jats:italic>P</jats:italic>. <jats:italic>azotoformans</jats:italic> SH3 being the most effective. All cell‐free filtrates inhibited mycelial growth with <jats:italic>B</jats:italic>. <jats:italic>velezensis</jats:italic> SH1 and SH2 resulting in the highest inhibition. The bacteria suppressed anthracnose lesions on strawberry fruit although effective treatments varied by causal mould. <jats:italic>B. velezensis</jats:italic> SH1 and SH2 significantly permeabilized spore membranes, indicating antibiosis as a possible mode of action. Investigation into antimicrobial compound production found various homologues of the lipopeptides fengycin, iturin and surfactin were produced by <jats:italic>B</jats:italic>. <jats:italic>velezensis</jats:italic> SH1 and SH2. Results suggest that lipopeptides produced by <jats:italic>B</jats:italic>. <jats:italic>velezensis</jats:italic> strains permeabilize <jats:italic>Colletotrichum</jats:italic> cell membranes, and that fengycins were the most inhibitory of the lipopeptides against <jats:italic>Colletotrichum</jats:italic> spp.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"38 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141969169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The fungi of Aspergillus section Flavi can produce carcinogenic mycotoxins—aflatoxins (AFs)—of two types: types B and G (AFBs and AFGs). AFs are highly hazardous for human and animal health. Their levels in food and feed are therefore highly regulated, with a low acceptable limit for AF content. In France, climate change has led to the detection of AFs in maize harvests since 2015. Mycoflora analyses have identified two species, A. flavus (producing AFBs) and A. parasiticus (producing both AFBs and AFGs), as responsible for this AF contamination. However, mycoflora analysis is a time‐consuming method that cannot readily be applied to large numbers of samples. We propose here an alternative clade‐specific functional TaqMan quantitative PCR method based on the calmodulin gene for distinguishing between the A. flavus clade (AfC) and the A. parasiticus clade (ApC). We applied this method to 553 maize samples collected in three different harvest years (2018–2020). Both clades were detected in about 40% of the samples tested. As expected, we observed significant positive correlations between AFBs and AfC DNA (R2 = 0.708), and between AFGs and ApC DNA (R2 = 0.885). This method will be useful for the rapid, simple and cheap characterization of maize grain contamination with Aspergillus section Flavi. This method will make it possible to study the relationship between agroclimatic conditions, AF content and species prevalence, to facilitate the anticipation of AF risks due to global warming in France.
黄曲霉科的真菌可产生致癌霉菌毒素--黄曲霉毒素（AFs），有两种类型：B 型和 G 型（AFBs 和 AFGs）。AFs 对人类和动物的健康危害极大。因此，它们在食品和饲料中的含量受到严格管制，AF 含量的可接受限值很低。在法国，自 2015 年以来，气候变化已导致在收获的玉米中检测到 AFs。霉菌群分析确定了两个物种，即黄曲霉（产生 AFBs）和寄生黄曲霉（同时产生 AFBs 和 AFGs），它们是造成这种 AF 污染的原因。然而，菌群分析是一种耗时的方法，无法随时应用于大量样本。我们在此提出了一种基于钙调蛋白基因的支系特异性功能 TaqMan 定量 PCR 方法，用于区分黄曲霉支系（AfC）和寄生虫支系（ApC）。我们在三个不同收获年份（2018-2020 年）收集的 553 份玉米样本中应用了该方法。在约 40% 的测试样本中检测到了这两个支系。正如预期的那样，我们观察到 AFB 与 AfC DNA 之间（R2 = 0.708）以及 AFGs 与 ApC DNA 之间（R2 = 0.885）存在显著的正相关性。该方法可用于快速、简便、廉价地鉴定玉米粒受弗拉维曲霉菌污染的情况。通过这种方法可以研究农业气候条件、AF 含量和物种流行之间的关系，从而有助于预测全球变暖给法国带来的 AF 风险。
{"title":"Two new qPCR assays for detecting and quantifying the Aspergillus flavus and Aspergillus parasiticus clades in maize kernels","authors":"Alexandre Leharanger, Delphine Paumier, Beatrice Orlando, Sylviane Bailly, Romain Valade","doi":"10.1111/ppa.13982","DOIUrl":"https://doi.org/10.1111/ppa.13982","url":null,"abstract":"The fungi of <jats:italic>Aspergillus</jats:italic> section <jats:italic>Flavi</jats:italic> can produce carcinogenic mycotoxins—aflatoxins (AFs)—of two types: types B and G (AFBs and AFGs). AFs are highly hazardous for human and animal health. Their levels in food and feed are therefore highly regulated, with a low acceptable limit for AF content. In France, climate change has led to the detection of AFs in maize harvests since 2015. Mycoflora analyses have identified two species, <jats:italic>A</jats:italic>. <jats:italic>flavus</jats:italic> (producing AFBs) and <jats:italic>A</jats:italic>. <jats:italic>parasiticus</jats:italic> (producing both AFBs and AFGs), as responsible for this AF contamination. However, mycoflora analysis is a time‐consuming method that cannot readily be applied to large numbers of samples. We propose here an alternative clade‐specific functional TaqMan quantitative PCR method based on the calmodulin gene for distinguishing between the <jats:italic>A</jats:italic>. <jats:italic>flavus</jats:italic> clade (AfC) and the <jats:italic>A</jats:italic>. <jats:italic>parasiticus</jats:italic> clade (ApC). We applied this method to 553 maize samples collected in three different harvest years (2018–2020). Both clades were detected in about 40% of the samples tested. As expected, we observed significant positive correlations between AFBs and AfC DNA (<jats:italic>R</jats:italic><jats:sup>2</jats:sup> = 0.708), and between AFGs and ApC DNA (<jats:italic>R</jats:italic><jats:sup>2</jats:sup> = 0.885). This method will be useful for the rapid, simple and cheap characterization of maize grain contamination with <jats:italic>Aspergillus</jats:italic> section <jats:italic>Flavi</jats:italic>. This method will make it possible to study the relationship between agroclimatic conditions, AF content and species prevalence, to facilitate the anticipation of AF risks due to global warming in France.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"4 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141940496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The use of repellents for nematode control has not been established. Leaf extracts of Myrtus communis, an evergreen shrub with wide distribution in the Mediterranean and some other regions, were tested for repellence of second‐stage juveniles (J2s) of Meloidogyne species. Extracts obtained with several solvents and water repelled M. javanica J2s on agar plates, with the 60% methanol extract showing the highest repellent activity. M. hapla J2s were also repelled by the aqueous and 60% methanol extracts. Adding the 60% methanol extract to fluopyram, a chemical J2 attractant, reduced and abolished, respectively, the attraction of M. javanica and M. hapla J2s to it. When the methanolic extract was added near lettuce seedling roots on an agar plate, the number of M. javanica, M. incognita and M. hapla J2s attracted to the root tips was reduced by 70.0%–98.2%, infection rates decreased by 50.1%–95.8% and root length increased by 61.8%–186.7% compared to control seedlings grown on the same plates. When the methanol extract was mixed into the agar plate, the three Meloidogyne species' attraction to and infection of lettuce seedlings was reduced by up to 75.4% and 100%, respectively, and root length increased up to 3.4‐fold. The acetone extract mixed into the agar reduced the attraction of M. javanica J2s to fluopyram but did not affect their repellence by KNO3. The results suggest that M. communis leaf extracts have repellent and infection‐inhibitory activity against Meloidogyne J2, offering potential control means for Meloidogyne species.
{"title":"Myrtus communis leaf extracts repel Meloidogyne spp. second‐stage juveniles and prevent root infection","authors":"Yuji Oka","doi":"10.1111/ppa.13981","DOIUrl":"https://doi.org/10.1111/ppa.13981","url":null,"abstract":"The use of repellents for nematode control has not been established. Leaf extracts of <jats:italic>Myrtus communis</jats:italic>, an evergreen shrub with wide distribution in the Mediterranean and some other regions, were tested for repellence of second‐stage juveniles (J2s) of <jats:italic>Meloidogyne</jats:italic> species. Extracts obtained with several solvents and water repelled <jats:italic>M</jats:italic>. <jats:italic>javanica</jats:italic> J2s on agar plates, with the 60% methanol extract showing the highest repellent activity. <jats:italic>M</jats:italic>. <jats:italic>hapla</jats:italic> J2s were also repelled by the aqueous and 60% methanol extracts. Adding the 60% methanol extract to fluopyram, a chemical J2 attractant, reduced and abolished, respectively, the attraction of <jats:italic>M</jats:italic>. <jats:italic>javanica</jats:italic> and <jats:italic>M</jats:italic>. <jats:italic>hapla</jats:italic> J2s to it. When the methanolic extract was added near lettuce seedling roots on an agar plate, the number of <jats:italic>M</jats:italic>. <jats:italic>javanica</jats:italic>, <jats:italic>M</jats:italic>. <jats:italic>incognita</jats:italic> and <jats:italic>M</jats:italic>. <jats:italic>hapla</jats:italic> J2s attracted to the root tips was reduced by 70.0%–98.2%, infection rates decreased by 50.1%–95.8% and root length increased by 61.8%–186.7% compared to control seedlings grown on the same plates. When the methanol extract was mixed into the agar plate, the three <jats:italic>Meloidogyne</jats:italic> species' attraction to and infection of lettuce seedlings was reduced by up to 75.4% and 100%, respectively, and root length increased up to 3.4‐fold. The acetone extract mixed into the agar reduced the attraction of <jats:italic>M</jats:italic>. <jats:italic>javanica</jats:italic> J2s to fluopyram but did not affect their repellence by KNO<jats:sub>3</jats:sub>. The results suggest that <jats:italic>M</jats:italic>. <jats:italic>communis</jats:italic> leaf extracts have repellent and infection‐inhibitory activity against <jats:italic>Meloidogyne</jats:italic> J2, offering potential control means for <jats:italic>Meloidogyne</jats:italic> species.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"56 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141940497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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