Concept Note: Toward Metagenomic Sequencing for Rapid, Sensitive, and Accurate Detection of Bacterial Pathogens in Potato Seed Production

Disease-free planting stocks and formal certification systems are critical for the profitable production of vegetatively propagated crops. Propagation through seed tubers is the standard and preferred process for potato production. Seed tuber certification systems are used in the United States and throughout the world to mitigate degeneration and promote the use of high-quality planting stocks. Seed certification uses molecular and serological diagnostic methods for stock testing. While the molecular assays available are well-validated and offer high sensitivity, the rapidly evolving pathogens they target routinely develop mutations that allow them to evade detection. Examples of these limitations are the potato diseases soft rot and blackleg, caused by Pectobacterium and Dickeya species. These diseases are challenging for current diagnostics tools because of high pathogen genomic variability, identical symptom development, and co-infections. Given the rapidly changing genetics of soft rot and blackleg bacteria, metagenomic sequencing should be adopted as a tool for routine validation of currently accepted diagnostic methods, and for the development of new diagnostic assays. We propose metagenome sequencing usage to enhance the diagnostic capabilities and complement molecular epidemiology approaches. We envision that metagenomics will accelerate diagnosis, shorten response time to outbreaks caused by unknown microorganisms, and provide more accurate and sustainable management strategies for seed certification programs. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .