scholarly journals Physics-informed deep learning characterizes morphodynamics of Asian soybean rust disease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Henry Cavanagh ◽  
Andreas Mosbach ◽  
Gabriel Scalliet ◽  
Rob Lind ◽  
Robert G. Endres
Keyword(s):  
Tip Growth ◽  
Soybean Rust ◽  
Population Development ◽  
Phakopsora Pachyrhizi ◽  
Biophysical Modeling ◽  
Top Down ◽  
Rust Disease ◽  
Asian Soybean Rust ◽  
2D Space ◽  
Shape Changes

AbstractMedicines and agricultural biocides are often discovered using large phenotypic screens across hundreds of compounds, where visible effects of whole organisms are compared to gauge efficacy and possible modes of action. However, such analysis is often limited to human-defined and static features. Here, we introduce a novel framework that can characterize shape changes (morphodynamics) for cell-drug interactions directly from images, and use it to interpret perturbed development of Phakopsora pachyrhizi, the Asian soybean rust crop pathogen. We describe population development over a 2D space of shapes (morphospace) using two models with condition-dependent parameters: a top-down Fokker-Planck model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. We discover a variety of landscapes, describing phenotype transitions during growth, and identify possible perturbations in the tip growth machinery that cause this variation. This demonstrates a widely-applicable integration of unsupervised learning and biophysical modeling.

scholarly journals Characterization of three soybean landraces resistant to Asian soybean rust disease

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Luciano Nobuhiro Aoyagi ◽  
Yukie Muraki ◽  
Naoki Yamanaka
Keyword(s):  
Susceptible Variety ◽  
Soybean Rust ◽  
Resistance Locus ◽  
Chromosome 6 ◽  
Phakopsora Pachyrhizi ◽  
Rust Disease ◽  
Asian Soybean Rust ◽  
The World ◽  
Trait Locus

Abstract Phakopsora pachyrhizi is an obligatory biotrophic fungus that causes Asian soybean rust (ASR) disease. ASR control primarily involves chemical control and the use of resistant soybean cultivars carrying an Rpp (resistance to P. pachyrhizi) gene. This study aimed to characterize the ASR resistance of three soybean Asian landraces. By screening the world core collection (WC) of soybean, which consists of 80 varieties, three landraces were identified in Southeast Asia as resistant to ASR. Genetic mapping using the F2 population derived from a cross with an ASR-susceptible variety, BRS 184, indicated that KS 1034 (WC2) has ASR resistance conferred by a single dominant resistance gene, mapped on chromosome 18, in the same region where Rpp1 was mapped previously. The BRS 184 × WC61 (COL/THAI/1986/THAI-80) F2 population, on the other hand, showed an ASR resistance locus mapped by quantitative trait locus analysis on chromosome 6, in the region where the resistance conferred by PI 416764 Rpp3 resides, with a logarithm of the odds score peak at the same position as the marker, Satt079, while the BRS 184 × WC51 (HM 39) population showed the resistance to ASR allocated between Satt079 and Sat_263 markers, also in the region where Rpp3 was mapped previously. Both WC51 and WC61 have the same infection profile as FT-2 and PI 462312 when tested against the same ASR isolate panel. These three WCs can be used in MAS programs for introgression of Rpp1 and Rpp3 and the development of ASR-resistant cultivars in the breeding program.

scholarly journals Identification and characterization of a new soybean promoter induced by Phakopsora pachyrhizi, the causal agent of Asian soybean rust

2020 ◽  
Author(s):  
Lisa Cabre ◽  
Stephane Peyrard ◽  
Catherine Sirven ◽  
Laurine Gilles ◽  
Bernard Pelissier ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Green Fluorescence Protein ◽  
Inducible Promoter ◽  
Soybean Rust ◽  
Limited Area ◽  
Phakopsora Pachyrhizi ◽  
Mechanical Wounding ◽  
Rust Disease ◽  
Asian Soybean Rust ◽  
Soybean Plants

ABSTRACTBackgroundPhakopsora pachyrhizi is a biotrophic fungal pathogen responsible for the Asian soybean rust disease causing important yield losses in tropical and subtropical soybean-producing countries. P. pachyrhizi triggers important transcriptional changes in soybean plants during infection, with several hundreds of genes being either up- or downregulated.ResultsBased on published transcriptomic data, we identified a predicted chitinase gene, referred to as GmCHIT1, that was upregulated in the first hours of infection. We first confirmed this early induction and showed that this gene was expressed as early as 8 hours after P. pachyrhizi inoculation. To investigate the promoter of GmCHIT1, transgenic soybean plants expressing the green fluorescence protein (GFP) under the control of the GmCHIT1 promoter were generated. Following inoculation of these transgenic plants with P. pachyrhizi, GFP fluorescence was detected in a limited area located around appressoria, the fungal penetration structures. Fluorescence was also observed after mechanical wounding whereas no variation in fluorescence of pGmCHIT1:GFP transgenic plants was detected after a treatment with an ethylene precursor or a methyl jasmonate analogue.ConclusionWe identified a soybean chitinase promoter exhibiting an early induction by P. pachyrhizi located in the first infected soybean leaf cells. Our results on the induction of GmCHIT1 promoter by P. pachyrhizi contribute to the identification of a new pathogen inducible promoter in soybean and beyond to the development of a strategy for the Asian soybean rust disease control using biotechnological approaches.

scholarly journals Identification and characterization of a new soybean promoter induced by Phakopsora pachyrhizi, the causal agent of Asian soybean rust

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
L. Cabre ◽  
S. Peyrard ◽  
C. Sirven ◽  
L. Gilles ◽  
B. Pelissier ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Green Fluorescence Protein ◽  
Inducible Promoter ◽  
Soybean Rust ◽  
Limited Area ◽  
Phakopsora Pachyrhizi ◽  
Mechanical Wounding ◽  
Rust Disease ◽  
Asian Soybean Rust ◽  
Soybean Plants

Abstract Background Phakopsora pachyrhizi is a biotrophic fungal pathogen responsible for the Asian soybean rust disease causing important yield losses in tropical and subtropical soybean-producing countries. P. pachyrhizi triggers important transcriptional changes in soybean plants during infection, with several hundreds of genes being either up- or downregulated. Results Based on published transcriptomic data, we identified a predicted chitinase gene, referred to as GmCHIT1, that was upregulated in the first hours of infection. We first confirmed this early induction and showed that this gene was expressed as early as 8 h after P. pachyrhizi inoculation. To investigate the promoter of GmCHIT1, transgenic soybean plants expressing the green fluorescence protein (GFP) under the control of the GmCHIT1 promoter were generated. Following inoculation of these transgenic plants with P. pachyrhizi, GFP fluorescence was detected in a limited area located around appressoria, the fungal penetration structures. Fluorescence was also observed after mechanical wounding whereas no variation in fluorescence of pGmCHIT1:GFP transgenic plants was detected after a treatment with an ethylene precursor or a methyl jasmonate analogue. Conclusion We identified a soybean chitinase promoter exhibiting an early induction by P. pachyrhizi located in the first infected soybean leaf cells. Our results on the induction of GmCHIT1 promoter by P. pachyrhizi contribute to the identification of a new pathogen inducible promoter in soybean and beyond to the development of a strategy for the Asian soybean rust disease control using biotechnological approaches.

scholarly journals First Report of Asian Soybean Rust Caused by Phakopsora pachyrhizi on Soybean in Alabama

Plant Disease ◽  
2006 ◽  
Vol 90 (1) ◽  
pp. 112-112 ◽  
Author(s):  
J. M. Mullen ◽  
E. J. Sikora ◽  
J. M. McKemy ◽  
M. E. Palm ◽  
L. Levy ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Rust Disease ◽  
First Report ◽  
Leaf Spots ◽  
Asian Soybean Rust ◽  
Leaf Surfaces ◽  
Soybean Leaves

On November 4, 2004, soybean leaves (Glycine max (L.) Merr) were submitted to the Auburn University Plant Diagnostic Lab by a State Department of Agriculture and Industries Inspector. Samples were collected from an 80-ha field of soybean plants in a late-reproductive-growth stage in Mobile County, Alabama. Under microscopic examination, leaves showed rust pustules in advanced stages of development with urediniospores and sori characteristic of Phakopsora spp. Uredinia were ostiolate in small, brown, angular leaf spots (2 to 3 mm) on lower leaf surfaces. Urediniospores were pale yellow-to-white, globose or ovate, 20 to 40 × 15 to 25 μm. In a subsequent visit to the field, symptoms and signs of the rust disease were observed on plants bordering the edge of the field since the majority of plants were senescent. Tan lesions on lower leaf surfaces contained small pustules surrounded by a small zone of slightly discolored necrotic tissue. Masses of tan spores covered the lower leaf surface pustules. Leaves were mailed overnight to the USDA National Identification Services (Mycology) Laboratory in Beltsville, MD. The fungal structures were confirmed to be a Phakopsora sp., and the sample was forwarded to the USDA National Plant Germplasm and Biotechnology Laboratory in Beltsville, MD. DNA was extracted from leaf pieces containing sori using the Qiagen DNeasy Plant Mini kit (Qiagen, Valencia, CA). Phakopsora pachyrhizi was detected using a real-time polymerase chain reaction (PCR) protocol (1) performed in a Cepheid SmartCycler (Sunnyvale, CA). The PCR master mix was modified to include OmniMix beads (Cepheid). The field and microscopic suspect diagnosis of P. pachyrhizi was confirmed officially by APHIS on November 18, 2004. This was the fourth USDA official confirmation of Asian soybean rust in the continental United States during 2004, and to our knowledge, this is the first report of the disease in Alabama. This report helps confirm that early occurrences of Asian soybean rust in the United States were present in other areas in addition to the first reported finding in Louisiana (2). References: (1) R. D. Frederick et al. Phytopathology 92:217, 2002. (2) R. W. Schneider et al. Plant Dis. 89:774, 2005.

scholarly journals Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

2013 ◽  
Vol 40 (10) ◽  
pp. 1029 ◽  
Author(s):  
Aguida M. A. P. Morales ◽  
Jamie A. O'Rourke ◽  
Martijn van de Mortel ◽  
Katherine T. Scheider ◽  
Timothy J. Bancroft ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Silencing ◽  
Differentially Expressed ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
R Gene ◽  
Virus Induced Gene Silencing ◽  
Asian Soybean Rust ◽  
Defence Responses

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.

scholarly journals Resistance to Asian soybean rust in soybean lines with the pyramided three Rpp genes

2013 ◽  
Vol 13 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Naoki Yamanaka ◽  
Noelle G Lemos ◽  
Miori Uno ◽  
Hajime Akamatsu ◽  
Yuichi Yamaoka ◽  
...  
Keyword(s):  
Genetic Background ◽  
Susceptible Variety ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Soybean Line ◽  
Pathogen Population ◽  
Resistance Level ◽  
Asian Soybean Rust ◽  
High Level

In this study, the influence of genetic background on the resistance level of a soybean line carrying Rpp2, Rpp4, and Rpp5 was evaluated by backcrossing it with a susceptible variety. It was also evaluated eight lines which carry these Rpp genes against five Asian soybean rust (ASR) isolates, in order to determine the likely range of resistance against ASR isolates differing in pathogenicity. The results indicated that a high level of resistance against various ASR isolates could be retained in lines carrying the three Rpp genes in susceptible genetic backgrounds, although minor influences of plant genetic background and ASR pathogenicity to the ASR resistance could occur. Thus, lines with the pyramided three Rpp genes should be effective against a complex pathogen population consisting of diverse Phakopsora pachyrhizi isolates.

scholarly journals Models and applications for risk assessment and prediction of Asian soybean rust epidemics

2006 ◽  
Vol 31 (6) ◽  
pp. 533-544 ◽  
Author(s):  
Emerson M. Del Ponte ◽  
Cláudia V. Godoy ◽  
Marcelo G. Canteri ◽  
Erlei M. Reis ◽  
X.B. Yang
Keyword(s):  
Disease Modeling ◽  
Weather Conditions ◽  
Epidemiological Studies ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Spatial And Temporal Scales ◽  
Asian Soybean Rust ◽  
New Development ◽  
Glycine Max L ◽  
Favorable Weather

Asian rust of soybean [Glycine max (L.) Merril] is one of the most important fungal diseases of this crop worldwide. The recent introduction of Phakopsora pachyrhizi Syd. & P. Syd in the Americas represents a major threat to soybean production in the main growing regions, and significant losses have already been reported. P. pachyrhizi is extremely aggressive under favorable weather conditions, causing rapid plant defoliation. Epidemiological studies, under both controlled and natural environmental conditions, have been done for several decades with the aim of elucidating factors that affect the disease cycle as a basis for disease modeling. The recent spread of Asian soybean rust to major production regions in the world has promoted new development, testing and application of mathematical models to assess the risk and predict the disease. These efforts have included the integration of new data, epidemiological knowledge, statistical methods, and advances in computer simulation to develop models and systems with different spatial and temporal scales, objectives and audience. In this review, we present a comprehensive discussion on the models and systems that have been tested to predict and assess the risk of Asian soybean rust. Limitations, uncertainties and challenges for modelers are also discussed.

Asian soybean rust: a scientometric approach of Phakopsora pachyrhizi studies

Euphytica ◽  
2020 ◽  
Vol 216 (8) ◽  
Author(s):  
Daniela Meira ◽  
Leomar Guilherme Woyann ◽  
Antonio Henrique Bozi ◽  
Anderson Simionato Milioli ◽  
Eduardo Beche ◽  
...  
Keyword(s):  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Asian Soybean Rust

scholarly journals Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing

Sequencing ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Arianne Tremblay ◽  
Parsa Hosseini ◽  
Nadim W. Alkharouf ◽  
Shuxian Li ◽  
Benjamin F. Matthews
Keyword(s):  
Soybean Rust ◽  
Cdna Libraries ◽  
Phakopsora Pachyrhizi ◽  
Rust Disease ◽  
Illumina Platform ◽  
Molecular Events ◽  
Genes Encoding ◽  
Exotic Pathogen ◽  
Soybean Leaves ◽  
Host Genes

Soybean rust is caused by the obligate biotrophic fungus Phakopsora pachyrhizi, an exotic pathogen causing important yield losses in soybean production. We used an mRNA-Seq strategy to analyze the expression pattern of soybean genes and better understand molecular events occurring in soybean following the infection. cDNA libraries were constructed from RNA isolated from whole infected soybean leaves 10 days after inoculation with P. pachyrhizi and sequenced using an Illumina platform to identify soybean genes that are affected by pathogen growth. We obtained 15 million sequences corresponding to soybean genes. Forty-two percent of the genes were downregulated including genes encoding proteins involved in amino acid metabolism, carbohydrate metabolism, and transport facilitation; 31% were upregulated including genes encoding proteins involved in lipid metabolism, glycan biosynthesis, and signal transduction. Candidate host genes identified in this study will be manipulated to assay their potential to control soybean rust disease.

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