Identification of the soybean HyPRP family and specific gene response to Asian soybean rust disease

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.

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

Nature Communications ◽

10.1038/s41467-021-26577-1 ◽

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.

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

10.1101/2020.06.07.138586 ◽

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.

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

BMC Biotechnology ◽

10.1186/s12896-021-00684-9 ◽

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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Correction to: Characterization of three soybean landraces resistant to Asian soybean rust disease

Molecular Breeding ◽

10.1007/s11032-020-01154-4 ◽

2020 ◽

Vol 40 (8) ◽

Author(s):

Luciano Nobuhiro Aoyagi ◽

Yukie Muraki ◽

Naoki Yamanaka

Keyword(s):

Soybean Rust ◽

Rust Disease ◽

Asian Soybean Rust

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Pengaruh Pemberian Agens Hayati Terhadap Intensitas Penyakit Karat Beberapa Varietas Kedelai Hitam

Daun Jurnal Ilmiah Pertanian dan Kehutanan ◽

10.33084/daun.v7i2.2011 ◽

2020 ◽

Vol 7 (2) ◽

pp. 117-125

Author(s):

Gayuh Prasetyo Budi ◽

Teguh Pribadi

Keyword(s):

Plant Growth Promoting Rhizobacteria ◽

Biological Agents ◽

Soybean Rust ◽

Rust Disease ◽

Black Soybean ◽

Asian Soybean Rust ◽

Randomized Design ◽

Resistant Varieties ◽

Plant Growth Promoting ◽

Corynebacterium Sp

Black soybean (G. max (L.) Merr.) is an important food crop and has a high nutritional content. Demand for this commodity is increasing. National soybean demand in 2015 about 2.6 million tons but domestic production only 982,967 tons. One of the obstacles to increasing black soybean production is Asian soybean rust disease caused by P. pachyrhizi. The susceptibility of black soybean to rust makes the farmers often use chemical fungicides to control it. Alternative control of rust leaves that suitable for the environment is through the selection of more resistant varieties of rust and the application of biological agents of Corynebacterium sp. and Plant Growth Promoting Rhizobacteria (PGPR). The research was conducted in endemic area of Asian soybean rust disease, using Complete Randomized Design 2 factors. Factor 1 varieties of black soybeans consists of V1: Detam 1, V2: Detam 3, V3: Detam 4 and Factor 2 biological agents consist of: control, Corynebacterium sp. and PGPR with 3 replications. The results showed that Detam 1 varieties produced the most massive seeds: 6.86 g plant-1. Corynebacterium sp. and PGPR treatment can significantly reduce the intensity of Asian soybean rust disease compared to controls. The intensity of rust disease in Corynebacterium sp. (11.7%), PGPR (8.9%), control (33.9%). Both soybean varieties and biological agents showed no interaction in all observed variables.

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

Plant Disease ◽

10.1094/pd-90-0112c ◽

2006 ◽

Vol 90 (1) ◽

pp. 112-112 ◽

Cited By ~ 5

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.

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