Molecular Diagnostics of Plant Pathogen Interactions

Molecular diagnostics of plant pathogen interactions encompasses a suite of nucleic acid–based and high-throughput sequencing techniques designed to detect, quantify and characterise pathogens and host responses with high sensitivity and specificity. Core approaches include polymerase chain reaction (PCR) and its quantitative real-time variants, digital PCR methods and transcriptome profiling. When complemented by microscopy and phenotypic assays, these tools enable early detection of fungal, bacterial and viral threats, guide breeding programmes for resistant cultivars and support sustainable disease management. Recent advances have integrated single-molecule detection, sequence-based marker development and effector discovery to map host–pathogen interfaces at unparalleled resolution. Such capabilities are critical for safeguarding global food security by reducing crop losses and informing targeted interventions in diverse agroecosystems.

Research from Nature Portfolio

Recent studies have characterised defence responses and refined detection methods in wheat–Tilletia pathosystems. One report described the molecular basis of resistance in distinct wheat cultivars, showing that resistant lines exhibit early and sustained expression of pathogenesis-related genes, enhanced callose deposition and delayed fungal hyphal ingress in reproductive tissues, as tracked by confocal microscopy. Another work employed RNA-sequencing of infected wheat spikes to reveal upregulation of defence-associated transcription factors, mitogen-activated protein kinases and salicylic acid-responsive networks, delineating key pathways activated upon Tilletia controversa infection. In addition, droplet digital PCR assays have been developed targeting species-specific DNA markers, achieving femtogram-level sensitivity for common bunt detection and enabling absolute quantification of pathogen load in seed and soil samples.

Molecular Diagnostics of Plant Pathogen Interactions publication trend

The graph below shows the total number of articles in molecular diagnostics of plant pathogen interactions across all publications each year (not limited to Nature Index journals).

Technical terms

Polymerase chain reaction (PCR): A method to amplify specific DNA sequences to detectable levels.

Quantitative real-time PCR (qPCR): A PCR variant that measures DNA amplification in real time, allowing quantification of target sequences.

Droplet digital PCR (ddPCR): A partition-based PCR technique that enables absolute quantification of nucleic acids at very low concentrations.

RNA-sequencing (RNA-seq): High-throughput sequencing of transcriptomes to profile gene expression changes during host–pathogen interactions.

Effector: A pathogen-derived molecule, often secreted, that modulates host immunity or physiology to promote infection.

References

1. Characterization of the wheat cultivars against Tilletia controversa Kühn, causal agent of wheat dwarf bunt. Scientific Reports (2020).
2. Transcriptome analysis of wheat spikes in response to Tilletia controversa Kühn which cause wheat dwarf bunt. Scientific Reports (2020).
3. Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR. Scientific Reports (2020).
4. Rapid molecular assay for the evaluation of clove essential oil antifungal activity against wheat common bunt. Frontiers in Plant Science (2023).
5. A DNA-based real-time PCR assay for robust growth quantification of the bacterial pathogen Pseudomonas syringae on Arabidopsis thaliana. Plant Methods (2016).
6. Development of a DNA-based real-time PCR assay for the quantification of Colletotrichum camelliae growth in tea (Camellia sinensis). Plant Methods (2020).