Seed World

Research Study Shows Benefits of Tracking Pathogens with Biomark X9 Amplicon Assays

Director of Marketing ,
Standard Biotools

Roberto Spada is the director of marketing at Standard BioTools. He holds a PhD in biochemistry and molecular biology from the University of Madrid.

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With more and more pathogens developing pesticide resistance, crop diseases are a major and growing threat to food production. Predicting how diseases will shape farming into the future depends on being able to identify genetic changes in pathogen populations. That’s increasingly efficient and cost-effective thanks to high-throughput amplicon assays achieved via the Biomark X9 system. But don’t take our word for it. In February last year, a team of researchers from French and Swiss Universities published a research study describing how they developed and validated a microfluidics-based multiplex targeted amplicon sequencing assay (using the Juno, an older version of the Biomark X9) for monitoring mutations in fungal plant pathogens. 

Their report highlights how the assay offers several advantages over traditional methods for ag-bio research, making it a valuable tool for studying and managing crop diseases. According to the authors, the advantages included:

  • Simultaneous monitoring of multiple loci: the assay can simultaneously assess hundreds of targeted loci, including genes associated with fungicide resistance, pathogenicity and genetic diversity. This comprehensive approach provides a more complete picture of the pathogen population and its evolution.
  • High-throughput and cost efficacy: the assay utilizes microfluidics technology to achieve high-throughput genotyping at a relatively low cost per sample. This makes it suitable for large-scale studies and routine monitoring of pathogen populations.
  • Reproducible and reliable results: the study demonstrates the assay’s reproducibility and reliability across different sample types, including pure fungal DNA, mixed samples, and DNA extracted directly from infected leaves. This ensures the accuracy and consistency of the data generated.
  • Effective performance with low-input DNA: the assay performs well even with low amounts of DNA, making it suitable for situations where obtaining large quantities of DNA is challenging.

The team used the assay to successfully multiplex 798 loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers for the fungal pathogen Zymoseptoria tritici, a major issue in wheat. The researchers optimized the primer design by integrating polymorphism data from 632 genomes of the same species, then tested the assay’s performance by genotyping 192 samples in two replicates. 

“Analysis of the short-read sequence data generated by the assay showed a fairly stable success rate across samples to amplify a large number of loci,” they said in their report. “The performance was consistent between samples originating from pure genomic DNA as well as material extracted directly from infected wheat leaves. In samples with mixed genotypes, we found that the assay recovers variations in allele frequencies. We also explored the potential of the amplicon assay to recover transposable element insertion polymorphism relevant for fungicide resistance. As a proof-of-concept, we show that the assay recovers the pathogen population structure across French wheat fields. Genomic monitoring of crop pathogens contributes to more sustainable crop protection and yields.”

Interested in learning more? Read more about our Biomark X9 system here or contact us at