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.

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 Pathogenic Variation of Phakopsora pachyrhizi Isolates on Soybean in the United States from 2006 to 2009

Plant Disease ◽  
2012 ◽  
Vol 96 (1) ◽  
pp. 75-81 ◽  
Author(s):  
M. Twizeyimana ◽  
G. L. Hartman
Keyword(s):  
United States ◽  
Resistance Genes ◽  
The United States ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Soybean Genotype ◽  
Pathogenic Variation ◽  
Differential Set ◽  
Soybean Genotypes ◽  
Soybean Leaves

The introduction of Phakopsora pachyrhizi, the cause of soybean rust, into the United States is a classic case of a pathogen introduction that became established in a new geographical region overwintering on a perennial host (kudzu, Pueraria lobata). The objective of our study was to classify the pathogenic variation of P. pachyrhizi isolates collected in the United States, and to determine the spatial and temporal associations. In total, 72 isolates of P. pachyrhizi collected from infected kudzu and soybean leaves in the United States were purified, then established and increased on detached soybean leaves. These isolates were tested for virulence and aggressiveness on a differential set of soybean genotypes that included six genotypes with known resistance genes (Rpp), one resistant genotype without any known characterized resistance gene, and a susceptible genotype. Three pathotypes were identified among the 72 U.S. P. pachyrhizi isolates based on the virulence of these isolates on the genotypes in the differential set. Six aggressiveness groups were established based on sporulating-uredinia production recorded for each isolate on each soybean genotype. All three pathotypes and all six aggressiveness groups were found in isolates collected from the southern region and from both hosts (kudzu or soybean) in 2008. Shannon's index based on the number of pathotypes indicated that isolates from the South region were more diverse (H = 0.83) compared with the isolates collected in other regions. This study establishes a baseline of pathogenic variation of P. pachyrhizi in the United States that can be further compared with variation reported in other regions of the world and in future studies that monitor P. pachyrhizi virulence in association to deployment of rust resistance genes.

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 Proteomic Analysis of Soybean Leaves in a Compatible and an Incompatible Interaction with Phakopsora Pachyrhizi

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Mateus Rodrigues Pereira ◽  
Bianca Castro Gouvêa ◽  
Francismar Corrêa Marcelino-Guimarães ◽  
Humberto Josué de Oliveira Ramos ◽  
Maurilio Alves Moreira ◽  
...  
Keyword(s):  
Control Measure ◽  
Production Costs ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Fructose Bisphosphate ◽  
Soybean Genotypes ◽  
Fructose Bisphosphate Aldolase ◽  
Soybean Leaves ◽  
Dimensional Electrophoresis ◽  
Carbonic Anhydrase 1

AbstractAsian soybean rust (ASR), which is incited by the fungus Phakopsora pachyrhizi, is considered one of the most aggressive diseases to the soybean culture. There are no commercial cultivars immune to the pathogen and the control measure currently used is the application of fungicides that harms the environment and increases production costs. For a better understanding of the host’s response to the pathogen at the molecular level, two soybean genotypes were analyzed (PI561356, resistant to ASR and Embrapa 48, susceptible) at 72 hours and 192 hours after inoculation with spores of P. pachyrhizi. Leaf protein profiles of the plants were compared by two-dimensional electrophoresis associated with mass spectrometry (MS). Twenty-two protein spots presented different levels when the two treatments were compared (inoculated vs. non-inoculated). From those, twelve proteins were identified by MS analysis. Some of them are involved in metabolic pathways related to plant defense against pathogens, as in the case of carbonic anhydrase, 1-deoxy-D-xylulose- 5-phosphate reductoisomerase, fructose-bisphosphate aldolase and glutamine synthetase. The possible biochemical-physiological meanings of our findings are discussed.

scholarly journals The Importance of Phenolic Metabolism to Limit the Growth of Phakopsora pachyrhizi

2009 ◽  
Vol 99 (12) ◽  
pp. 1412-1420 ◽  
Author(s):  
Anatoliy V. Lygin ◽  
Shuxian Li ◽  
Ramya Vittal ◽  
Jack M. Widholm ◽  
Glen L. Hartman ◽  
...  
Keyword(s):  
Protective Role ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Phenolic Metabolism ◽  
Rust Infection ◽  
Resistant Lines ◽  
Significant Difference ◽  
Soybean Genotypes ◽  
Soybean Leaves

Understanding the metabolic responses of the plant to a devastating foliar disease, soybean rust, caused by Phakopsora pachyrhizi, will assist in development of cultivars resistant to soybean rust. In this study, differences in phenolic metabolism were analyzed between inoculated and noninoculated plants using two susceptible and three resistant soybean genotypes with known resistance genes. Rust infection resulted in increased accumulation of isoflavonoids and flavonoids in leaves of all soybean genotypes tested. Although the soybean phytoalexin glyceollin was not detected in leaves of uninfected plants, accumulation of this compound at marked levels occurred in rust-infected leaves, being substantially higher in genotypes with a red-brown resistant reaction. In addition, there was inhibition of P. pachyrhizi spore germination by glyceollin, formononetin, quercetin, and kaempferol. However, there was no correlation between concentrations of flavonoids quercetin and kaempferol and rust-induced isoflavonoid formononetin in soybean leaves and rust resistance. Lignin synthesis also increased in all inoculated soybean genotypes whereas there was no significant difference in all noninoculated soybean genotypes. Cell wall lignification was markedly higher in inoculated resistant lines compared with inoculated susceptible lines, indicating a possible protective role of lignin in rust infection development.

scholarly journals Effects of Simplicillium lanosoniveum on Phakopsora pachyrhizi, the Soybean Rust Pathogen, and Its Use as a Biological Control Agent

2012 ◽  
Vol 102 (8) ◽  
pp. 749-760 ◽  
Author(s):  
N. A. Ward ◽  
C. L. Robertson ◽  
A. K. Chanda ◽  
R. W. Schneider
Keyword(s):  
Biological Control Agent ◽  
Signs And Symptoms ◽  
Control Agent ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
Latent Stage ◽  
Leaf Surfaces ◽  
Rust Pathogen ◽  
Soybean Leaf ◽  
Soybean Leaves

The fungus Simplicillium lanosoniveum was isolated from soybean leaves infected with Phakopsora pachyrhizi, the soybean rust pathogen, in Louisiana and Florida. The fungus did not grow or become established on leaf surfaces until uredinia erupted, but when soybean rust signs and symptoms were evident, S. lanosoniveum colonized leaves within 3 days and sporulated within 4 days. Development of new uredinia was suppressed by about fourfold when S. lanosoniveum colonized uredinia. In the presence of S. lanosoniveum, uredinia became increasingly red-brown, and urediniospores turned brown and germinated at very low rates. Assays using quantitative real time polymerase chain reaction revealed that the fungus colonized leaf surfaces when plants were infected with P. pachyrhizi, either in a latent stage of infection or when symptoms were present. However, when plants were inoculated before infection, there was no increase of DNA of S. lanosoniveum, suggesting that the pathogen must be present in order for the antagonist to become established on soybean leaf surfaces. We documented significantly lower amounts of DNA of P. pachyrhizi and lower disease severity when soybean leaves were colonized with S. lanosoniveum. These studies documented the mycophilic and disease-suppressive nature of S. lanosoniveum.

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 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.

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