Molecular Biology and Omic Technologies in the Identification of Plants, Plant Derived-Products, Plant Pathogens, and Plant Microbiomes

Molecular characterization is a key process in classifying and identifying plants, plant-derived products, plant pathogens, and the associated microbiomes. The polymorphisms found among organisms can provide phylogenetic signal but are also important in the regulatory context of trade, as well as in epidemiology, ecological, and population studies. Nowadays, the determination of plant mixed products, plant species or varieties, and associated pathogens (races and pathotypes) and microbiomes, or the distinction between closely related regulated vs. non-regulated organisms, requires efficient and high-throughput tools. The advances in barcoding and metabarcoding, as well as other DNA-based identification, implemented through PCR-based assays, high-throughput sequencing technologies, and other omic and molecular biology tools, have positively impacted our diagnostic ability. This in turn benefits risk assessment and regulatory action impacting our natural environment, our agriculture and forestry sectors, and human health.

Currently, international regulatory frameworks are not standardized to use molecular and omic tools for plant and plant pathogen identification, in part due to differences in technology access. There are also limitations within each country in terms of the access that different stakeholders (academic, industry, government, and farmers) can have to the use of these tools to perform molecular-based diagnostics and make better in-season management decisions. While phenotypic characterization can work in some cases and has been widely used for years both for regulation and management, many of the traditional phenotypical approaches take a long time or are unavailable for certain organisms. For example, characterizing weed seeds in bulk seed samples sometimes requires extensive time from seed analysts or even the need to grow the plant. Also, it is impossible to culture certain pathogens, and challenges in detecting food contaminants in processed products require molecular tools. Furthermore, there is an intrinsic and specific relationship between plant-pathogens-microbiomes that often goes beyond the species level, making it necessary to have molecular tools for the classification of subspecies, varieties, races, and pathotypes.

Within the scope of the title and defined goal, the following specific technologies and methodologies can be explored in original research, review, or method articles:

• DNA, protein, or metabolite profiling
• Molecular and omics diagnostics
• Omic technologies
• Bioinformatics tools for molecular identification and diagnostics
• High-throughput Sequencing
• Phylo-molecular analyses

Disclaimer: Comparative omic analyses that only report a collection of differentially expressed e.g. genes/metabolites/proteins, some validated by qPCR under different conditions or treatments; will also not be considered for review. They can be considered if extended to provide meaningful insights into gene/protein function and/or the biology of the subject described.