PCR-based simple sequence repeat markers for diagnostic identification of major clonal lineages of Puccinia striiformis f. sp. tritici and related stripe rust pathogens in Australia

Bailey, James; Karaoglu, Haydar; Wellings, C. R.; Park, Robert

doi:10.1007/s13313-014-0326-3

Cited by 8 publications

(5 citation statements)

References 17 publications

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“…In this experiment, the detection limit varied considerably among the presented PCR assays. A similar range of fungal DNA detection (2 pg/μL to 2 ng/μL) was found using simple sequence repeat markers developed for the diagnosis of stripe rust in Australia [Bailey et al, 2015]. PCR assays by other study groups [Liu et al 2015;Wang et al, 2008] revealed similar sensitivities to the lowest detection limit for Pst (10 pg/μL) whereas for Pr (0.1 to 1 pg/μL), the available tests showed weaker sensitivity when studying pure fungal DNA, or its mixture with wheat DNA [Cao et al, 2007;Fraaije et al, 2001].…”

Section: Discussionsupporting

confidence: 57%

Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases: Puccinia triticina and Puccinia striiformis f. sp. tritici

Kuzdraliński

Kot²,

Szczerba³

et al. 2017

Microb Physiol

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The species Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst) are devastating cereal pathogens that cause leaf and stripe rust diseases. We developed PCR assays for the species-specific detection of Pt and Pst, 2 biological agents that cause wheat rust disease. For each pathogen, we validated 3 primer sets that target the second largest subunits of the RNA polymerase II (rpb2) and β-tubulin 1 (tub1) genes. The specificities of the primers were verified using naturally infected plant materials with visual symptoms of disease. All primer sets amplified a single DNA fragment of the expected length. The primer sets LidPr15/16, LidPr1/2, and LidPs13/14 were able to detect small amounts of pure fungal DNA with sensitivities of 0.1, 1, and 10 pg/μL, respectively. A sufficient detection limit (1 pg/μL to 5 ng/μL) was observed for all assays when the sensitivity test was performed with host plant DNA. The study also evaluated the simultaneous detection of both rust pathogens, and the multiplex PCR assay generated amplicons of 240 and 144 bp in length for Pts (LidPs9/10) and Pt (LidPr1/2), respectively.

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Section: Discussionsupporting

confidence: 57%

Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases: Puccinia triticina and Puccinia striiformis f. sp. tritici

Kuzdraliński

Kot²,

Szczerba³

et al. 2017

Microb Physiol

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“…The use of SSR markers in diagnostic identification of fungal species is still widely employed for both rapid pathogen identification in response to incursions, and for analysis of population genetic diversity [ 34 , 35 , 36 , 37 ]. These markers are also widely used for identification of Epichloë endophytes in Pooideae grasses [ 38 , 39 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events

et al. 2017

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Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

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“…The success of efficient SSR based monitoring of stripe rust pathogen using only 9 loci in wheat in Australia clearly demonstrates that rapid and efficient pathogen identification with minimum risk and time constraints associated with screening of exotic isolates [ 48 ] in quarantine centers at port of entry. Such screening has to be robust, reproducible, even with limited DNA quantities.…”

Section: Resultsmentioning

confidence: 99%

Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

Iquebal

Jaiswal

Mishra

et al. 2021

JoF

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Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.

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PCR-based simple sequence repeat markers for diagnostic identification of major clonal lineages of Puccinia striiformis f. sp. tritici and related stripe rust pathogens in Australia

Cited by 8 publications

References 17 publications

Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases:<b><i> Puccinia triticina</i></b> and <b><i>Puccinia striiformis</i></b> f. sp. <b><i>tritici</i></b>

Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases:<b><i> Puccinia triticina</i></b> and <b><i>Puccinia striiformis</i></b> f. sp. <b><i>tritici</i></b>

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events

Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

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