Related Experiment Video
Updated: Jun 22, 2026
A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica
Published on: February 20, 2012
Eight Novel Diagnostic Markers Differentiate Lineages of the Highly Invasive Myrtle Rust Pathogen Austropuccinia
Zhenyan Luo1, Jinghang Feng1, Austin Bird1
1Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
Abstract:
Austropuccinia psidii is the causal agent of myrtle rust in more than 480 species within the family Myrtaceae. Lineages of A. psidii are structured by their hosts in the native range, and some have success in infecting newly encountered hosts. For example, the pandemic biotype has spread beyond South America, and proliferation of other lineages is an additional risk to biodiversity and industries. Efforts to manage A. psidii incursions, including lineage differentiation, rely on variable microsatellite markers. Testing these markers is time-consuming and complex and requires reference material that is not always readily available. We designed a novel diagnostic approach targeting eight selectively chosen loci including the fungal mating-type HD (homeodomain) transcription factor locus. The HD locus (bW1/2-HD1 and bE1/2-HD2) is highly polymorphic, facilitating clear biological predictions about its inheritance from founding populations. To be considered as potentially derived from the same lineage, all four HD alleles must be identical. If all four HD alleles are identical, six additional markers can further differentiate lineage identity. Our lineage diagnostics relies on PCR amplification of eight loci in different genotypes of A. psidii followed by amplicon sequencing using Oxford Nanopore Technologies and comparative analysis. The lineage-specific assay was validated on four isolates with existing genomes, on uncharacterized isolates, and directly from infected leaf material. We reconstructed alleles from amplicons and confirmed their sequence identity relative to their reference. Genealogies of alleles confirmed the variations at the loci among lineages/isolates. Our study establishes a robust diagnostic tool for differentiating known lineages of A. psidii based on biological predictions and available nucleotide sequences. This tool is suited to detecting the origin of new pathogen incursions.
Insights
A new diagnostic tool accurately differentiates myrtle rust (Austropuccinia psidii) lineages using eight genetic markers, including the homeodomain locus. This method aids in tracking pathogen spread and managing incursions.
Area of Science:
- Plant Pathology
- Molecular Diagnostics
- Fungal Genetics
Background:
- Myrtle rust, caused by *Austropuccinia psidii*, affects over 480 Myrtaceae species.
- Pathogen lineages vary in host range and spread, posing risks to biodiversity and industry.
- Existing microsatellite markers for lineage differentiation are complex and require reference material.
Purpose of the Study:
- To develop a novel, robust diagnostic approach for differentiating *A. psidii* lineages.
- To establish a tool for rapid identification of pathogen origins and management of incursions.
Main Methods:
- Designed a diagnostic assay targeting eight loci, including the polymorphic homeodomain (*HD*) transcription factor locus.
- Utilized PCR amplification, Oxford Nanopore Technologies amplicon sequencing, and comparative analysis.
- Validated the assay on known isolates, uncharacterized isolates, and infected leaf material.
Main Results:
- The *HD* locus and six additional markers effectively differentiate *A. psidii* lineages.
- Alleles were reconstructed from amplicons, confirming sequence identity and variations among lineages.
- The assay demonstrated robustness across various sample types.
Conclusions:
- A reliable diagnostic tool for *A. psidii* lineage differentiation has been established.
- The tool leverages biological predictions and sequence data for accurate identification.
- This assay is crucial for detecting new pathogen incursions and informing management strategies.
More Related Videos
07:09A Rapid and Efficient Method for Assessing Pathogenicity of Ustilago maydis on Maize and Teosinte Lines
Published on: January 3, 2014
11:48A Contrast of Three Inoculation Techniques used to Determine the Race of Unknown Fusarium oxysporum f.sp. niveum Isolates
Published on: October 28, 2021
