Kaique S. Alves

Universidade Federal de Viçosa

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Emerson M. Del Ponte

Universidade Federal de Viçosa

Willian Bucker Moraes

Universidade Federal do Espírito Santo

João Paulo Ascari

Fundação de Amparo à Pesquisa do Estado de Mato Grosso

Jhonatan Paulo Barro

Universidade Federal de Viçosa

Hiago Antonio Oliveira da Silva

Universidade Federal de Viçosa

Zachary Foster

Horticultural Crops Research Laboratory

Adam Sparks

University of Southern Queensland

Franklin Jackson Machado

Universidade Federal de Viçosa

Paul D. Esker

Pennsylvania State University

Mariana Guimarães

Universidade Federal de Goiás

Cooperative Institutions

Universidade Federal de Viçosa

Universidade Federal do Espírito Santo

Brazilian Agricultural Research Corporation

Agricultural Research Service

Universidade Federal de Lavras

United States Department of Agriculture

Universidade de São Paulo

Universidade do Vale do Paraíba

Centro Latino-Americano e do Caribe de Informação em Ciências da Saúde

Universidade Federal do Rio Grande do Sul

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Openness and Computational Reproducibility in Plant Pathology: Where we Stand and a Way Forward

Adam Sparks Emerson M. Del Ponte Kaique S. Alves Zachary Foster Niklaus J. Grünwald

Openness and computational reproducibility in plant pathology: where do we stand and a way forward. Abstract Open research practices have been highlighted extensively during the last ten years in many fields of scientific study as essential standards needed to promote transparency and reproducibility of scientific results. Scientific claims can only be evaluated based on how protocols, materials, equipment and methods were described; data were collected and prepared; and analyzes were conducted. Openly sharing protocols, data and computational code is central for current scholarly dissemination and communication, but in many fields, including plant pathology, adoption of these practices has been slow. We randomly selected 450 articles published from 2012 to 2021 across 21 journals representative of the plant pathology discipline and assigned them scores reflecting their openness and computational reproducibility. We found that most of the articles were not following protocols for open science and were failing to share data or code in a reproducible way. We also propose that use of open-source tools facilitates computationally reproducible work and analyzes benefitting not just readers, but the authors as well. Finally, we also provide ideas and tools to promote open, reproducible computational research practices among plant pathologists. Open preprint This article is a preprint and has not been peer reviewed

Openness to experience

Preprint

Open Science

Best practice

10.31220/agrirxiv.2021.00082

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Citations (1)

Sequential Post-Heading Applications for Controlling Wheat Blast: A 9-Year Summary of Fungicide Performance in Brazil

Plant Disease (2021)

João Paulo Ascari Jhonatan Paulo Barro F. M. Santana José Maria Villela Pádua João Leodato Nunes Maciel

Wheat blast, caused by Pyricularia oryzae Triticum lineage, is a major constraint to wheat production, mainly in the tropics of Brazil, where severe epidemics have been more frequent. We analyzed disease and wheat yield data from 42 uniform field trials conducted over 9 years (2012 to 2020) to assess whether the percent control and yield response were influenced by fungicide type, region (tropical or subtropical), and year. Six treatments were selected, all evaluated in at least 19 trials. Two fungicides were applied as solo active ingredients (MANCozeb, and TEBUconazole), and four were premixes (AZOXystrobin plus TEBU, TriFLoXystrobin plus PROThioconazole, TFLX plus TEBU, and PYRAclostrobin plus EPOXiconazole). Percent control, calculated from back-transforming estimates by a meta-analysis network model fitted to the log of the means, ranged from 43 to 58%, with all but PYRA plus EPOX showing efficacy >52% on average, not differing among them. The variation in both efficacy and yield response was explained by region, and all but TEBU performed better in the subtropics than in the tropics. Yield response from using three sequential sprays was approximately two times greater in the subtropics (319 to 532 kg/ha) than in the tropics (149 to 241.3 kg/ha). No significant decline in fungicide efficacy or yield response was observed in 9 years of study for any of the fungicides. These results reinforce the need to improve control by adopting an integrated management approach in the tropics given poorer performance and lower profitability, especially for the premixes, than in the subtropics.

Pyricularia

Tebuconazole

10.1094/pdis-06-21-1183-re

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Citations (23)

AVALIAÇÃO DA EFICÁCIA DE ÓLEO ESSENCIAL DE CANELA SOBRE A INIBIÇÃO DO CRESCIMENTO MICELIAL DE Botrytis cinerea

30ª SEAGRO: ANAIS DA SEMANA ACADÊMICA DO CURSO DE AGRONOMIA DO CCAE/UFES (2017)

Isadora Rodrigues Garcia Guilherme Bravim Canal Rodolfo Ferreira de Mendonça Kaique S. Alves Vagner Tebaldi de Queiroz

Os oleos essenciais sao compostos volateis que possuem atividade antimicrobiana e nao sao agressivos a saude e ao meio ambiente. O trabalho objetivou avaliar o efeito inibitorio do oleo essencial de canela sobre o crescimento micelial de Botrytis cinerea . Utilizou-se o delineamento experimental inteiramente casualizado com 5 tratamentos de oleo essencial de canela ( Cinnamomum zeilanicum ) nas concentracoes de 250, 500, 750 e 1000 mg/L de meio de cultura, e um fungicida como tratamento adicional. O oleo essencial e o fungicida mancozeb (750 g/Kg) na concentracao de 3000 mg/L foram fundidos ao meio de cultura BDA. Adicionou-se um disco de micelio no centro das placas de Petri que permaneceram em câmara BOD ate que a testemunha atingisse o diâmetro total da placa, e mediu-se o diâmetro das colonias fungicas. O oleo essencial de canela apresentou, a partir da concentracao de 500 mg/L, inibicao completa do crescimento micelial. Diante disso, conclui-se que o oleo essencial de canela foi eficiente do controle do patogeno a partir de 500 mg/L.

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Disentangling environmental effects on plant disease epidemics at the regional scale

Kaique S. Alves

The environment plays an essential role in driving the occurrence and dynamics of plant disease epidemics. The weather is known to influence pathogen and host biology and should modulate the stages of the disease cycle. On the other hand, climate, the average of weather within long periods of time (i.e. 30 years), should set the predominance of pathogens and host genotypes across regions, and therefore the spatial distribution of plant diseases and their respective intensities. In this thesis, three studies aiming to unravel the effects of environmental factors on plant disease epidemics will be presented. The first study will demonstrate how the climate shapes the spatial distribution of citrus Huanglongbing prevalence in Minas Gerais. In the second study, the time to onset of soybean rust in commercial soybean fields from Southern Brazil was associated with the El Nino Southern Oscillation, a phenomenon that triggers extreme weather events around the globe and also in Brazil; The third study integrates cutting- edge statistical methodology to associate weather time series and soil properties data to white mold prevalence in snap bean fields in New York, United States. The results led to novel insights into pathogen biology and disease risk at the regional and local scales for the three pathosystems under study. Keywords: Epidemiology. Huanglongbing. Soybean rust. White mold. Bayesian. Machine learning.

Plant disease

10.47328/ufvbbt.2023.053

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epifitter: an R package for the analysis and simulation of plant disease progress curves

Kaique S. Alves Emerson M. Del Ponte

10.17605/osf.io/xkfym

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Lipopeptide-enriched extracts of Bacillus velezensis B157 for controlling tomato early blight

Crop Protection (2023)

Amarildo L. da Silva Álefe Vitorino Borges Hiago Antonio Oliveira da Silva Iris Carolina Henrique de Lima Leite Kaique S. Alves

Lipopeptide

Alternaria solani

Plant disease

Secondary metabolite

Bacillus (shape)

Phytophthora infestans

10.1016/j.cropro.2023.106317

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Citations (6)

Modeling Yield Losses and Fungicide Profitability for Managing Fusarium Head Blight in Brazilian Spring Wheat

Phytopathology (2019)

Maíra Rodrigues Duffeck Kaique S. Alves Franklin Jackson Machado Paul D. Esker Emerson M. Del Ponte

Fusarium head blight (FHB) and wheat yield data were gathered from fungicide trials to explore their relationship. Thirty-seven studies over 9 years and 11 locations met the criteria for inclusion in the analysis: FHB index in the untreated check ≥ 5% and the range of index in a trial ≥ 4 percentage points. These studies were grouped into two baseline yields, low (Yl ≤ 3,631 kg ha-1) or high (Yh > 3,631 kg ha-1), defined based on the median of maximum yields across trials. Attainable (disease-free) yields and FHB index were predicted using a wheat crop and a disease model, respectively, in 280 simulated trials (10 planting dates in a 28-year period, 1980 to 2007) for the Passo Fundo location. The damage coefficient was then used to calculate FHB-induced yield loss (penalizing attainable yield) for each experiment. Losses were compared between periods defined as before and after FHB resurge during the early 1990s. Disease reduction from the use of one or two sprays of a triazole fungicide (tebuconazole) was also simulated, based on previous meta-analytic estimates, and the response in yield was used in a profitability analysis. Population-average intercepts but not the slopes differed significantly between Yl (2,883.6 kg ha-1) and Yh (4,419.5 kg ha-1) baseline yields and the damage coefficients were 1.60%-1 and 1.05%-1, respectively. The magnitudes and trends of simulated yield losses were in general agreement with literature reports. The risk of not offsetting the costs of one or two fungicide sprays was generally higher (>0.75) prior to FHB resurgence but fungicide profitability tended to increase in recent years, depending on the year. Our simulations allowed us to reproduce trends in historical losses, and may be further adjusted to test the effect and profitability of different control measures (host resistance, other fungicides, etc.) on quality parameters such as test weight and mycotoxin contamination, should the information become available.

Tebuconazole

10.1094/phyto-04-19-0122-r

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Citations (26)

Performance of dual and triple fungicide premixes for managing soybean rust across years and regions in Brazil: A meta‐analysis

Plant Pathology (2021)

Jhonatan Paulo Barro Kaique S. Alves C. V. Godoy A. R. Dias Carlos Alberto Forcelini

Abstract Soybean rust in Brazil is currently controlled with several commercial fungicide premixes composed of demethylation inhibitors (EPOXiconazole, CYPRoconazole, PROThioconazole, TEBUconazole), quinone‐outside inhibitors (AZOXystrobin, TriFLoXystrobin, PYRAclostrobin, PICOxystrobin), and succinate demethylation inhibitors (BENZovindiflupyr, BIXaFen, FLUXapyroxad). Here, we summarize the performance of eight premixes evaluated in 177 cooperative trials conducted in 46 locations across 10 states from 2015 to 2020. All fungicide treatments were sprayed three times starting at R1/R2. Percentage control ( , %), from back‐transforming meta‐analytic estimates of the log of the ratio, ranged from 56.2% (PICO + CYPR) to 76.8% (BIXF + TFLX + PROT). Estimates of mean yield difference ( , kg/ha) between fungicide‐treated and untreated plots were greatest for BIXF + TFLX + PROT (1,080) followed by PICO + BENZ (1,010), PYRA + EPOX + FLUX (981.5), AZOX + BENZ (910), TFLX + PROT (891), PICO +TEBU (682), TFLX + CYPR (646), and PICO + CYPR (600). Significant declines in both and in as little as 4 years were detected for AZOX + BENZ (35.3%; 550 kg/ha) and PICO + BENZ (15.5%; 359.8 kg/ha). Variance in was reduced by the inclusion of baseline severity as covariate. In trials where baseline disease was ≥70%, yield was 250 kg/ha greater compared to areas with low baseline disease. Disease control and yield response were generally greater in the south‐east, where the frequency of profitable scenarios was 30% higher on average than in the north‐west. Results of this meta‐analysis are critical for supporting decisions during planning of fungicide programmes.

Tebuconazole

Demethylation

10.1111/ppa.13418

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Citations (15)

Biocontrol of potato early blight and suppression of Alternaria grandis sporulation by Clonostachys spp.

Plant Pathology (2021)

Hiago Antonio Oliveira da Silva William D. Teixeira Álefe Vitorino Borges Amarildo L. da Silva Kaique S. Alves

Abstract Early blight, caused by Alternaria solani and A . grandis , severely affects potato crops around the world, and few management options apart from intensive fungicide use are available. In this work, we tested whether biocontrol treatments with different species of the mycoparasitic fungus Clonostachys could reduce early blight severity on the foliage of pot‐grown potatoes of cultivar Ágata, and affect the survival and sporulation of the causal pathogen A . grandis . Twenty isolates from five Clonostachys species were screened in a preliminary biocontrol trial, and nine of them were selected and tested further in two confirmation trials. Treatments with three isolates from three species ( C . chloroleuca , C . pseudochroleuca , C . rhizophaga ) resulted in a significant reduction in disease severity in both confirmation trials, with control efficacy ranging from 88.7% to 92.9% in the first trial, and from 83.1% to 84.7% in the second trial. All Clonostachys isolates used in the confirmation trials survived on potato leaf tissues for at least 15 days, and resumed growth when subjected to high humidity, resulting in mycoparasitic overgrowth and significant reduction of the pathogen sporulation. Our results provide evidence that different species of Clonostachys , not only the ubiquitous C . rosea , are sources of useful candidates for the biocontrol of potato early blight and possibly other plant diseases caused by fungal pathogens.

Alternaria solani

10.1111/ppa.13402

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Citations (18)

Research Compendium: Biocontrol of Potato Early Blight with different Clonostachys spp. species

Kaique S. Alves Hiago Antonio Oliveira da Silva

Compendium

Entomophthorales

10.17605/osf.io/f7vpb

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