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Kashyap PL, Kumar S, Kumar RS, Sharma A, Jasrotia P, Singh DP, Singh GP. Molecular Diagnostic Assay for Rapid Detection of Flag Smut Fungus ( Urocystis agropyri) in Wheat Plants and Field Soil. FRONTIERS IN PLANT SCIENCE 2020; 11:1039. [PMID: 32754183 PMCID: PMC7366794 DOI: 10.3389/fpls.2020.01039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Flag smut incited by Urocystis agropyri has the potential to cause substantial reduction in yield and quality of wheat production. An early and precise diagnosis is a key component in the successful management of flag smut of wheat. Therefore, a simple molecular assay for the rapid detection of U. agropyri was developed for the first time. To detect U. agropyri, species specific primers were developed by comparing the partial sequences of internal transcribed spacer (ITS) DNA region of U. agropyri with related and unrelated phytopathogenic fungi. The clear amplicons of 503 and 548 bp were obtained with the two sets of designed primers (UA-17F/UA-519R and UA-15F/UA-562R) from the genomic DNA of 50 geographic distinct isolates of U. agropyri. However, no amplicon was obtained from the DNA of other 21 related and unrelated phytopathogenic fungi which showed the specificity of the primers for the U. agropyri. PCR reaction was also set up to confirm the presence of U. agropyri spores in six different wheat varieties along with eleven distinct regional soil samples as template DNA. The presence of U. agropyri in all the soil samples collected from an infected field and plant tissue of diseased plants collected at two different stages (20 and 40 days post sowing) and the absence in the soils and plants of healthy plots indicated 100% reliability for detection of U. agropyri. This simple and rapid test can be employed for the detection of U. agropyri from enormous wheat and soil samples in very short time with less man power. Thus, the reported molecular assay is very specific for U. agropyri and requires less time and man power over conventional diagnosis which is often confused by coinciding morphological features of closely related fungal pathogens, and therefore, it can be used for quarantine surveillance of flag smut.
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Affiliation(s)
| | - Sudheer Kumar
- *Correspondence: Prem Lal Kashyap, ; ; Sudheer Kumar,
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Kashyap PL, Kumar S, Tripathi R, Kumar RS, Jasrotia P, Singh DP, Singh GP. Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat. Front Microbiol 2019; 10:1072. [PMID: 31156587 PMCID: PMC6529584 DOI: 10.3389/fmicb.2019.01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (IA = 1.169) and standardized index of association (rBarD = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (Fst = 0.012). Recombination (Rm = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.
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Affiliation(s)
- Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Rahul Tripathi
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Ravi Shekhar Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Poonam Jasrotia
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Devendra Pal Singh
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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