A multi-omics approach to solving problems in plant disease ecology

Abstract

The swift rise of omics-approaches allows for investigating microbial diversity and plantmicrobe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating-omic approaches into their plant disease research. We review-omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multiomics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.

Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses

“…The Omics approach offers the possibility to identify and characterize proteins and genes, which could be useful to select promising strains as biopesticides, plant growth promoters, etc. In addition, metagenomic analyses have been used to investigate the microbial diversity associated with plants under several environmental conditions [ 271 ]. Furthermore, metagenomic analyses enable investigating the microbiome in plant health in crops and natural system [ 271 ].…”

“…In addition, metagenomic analyses have been used to investigate the microbial diversity associated with plants under several environmental conditions [ 271 ]. Furthermore, metagenomic analyses enable investigating the microbiome in plant health in crops and natural system [ 271 ]. Although the focus of the current review is not the Omics approach, it is important for understanding the endophyte–plant interactions and their possible use in agriculture.…”

Plant Disease Sensing: Studying Plant-Pathogen Interactions at Scale

“…This article has thus far focused on the benefits plant disease sensing can provide to agriculture; however, fundamental research in this domain stands to benefit multiple disciplines. Spectranomics can be thought of as a light-based DNA sequence, capturing both a plant’s current state of existence and its evolutionary history ( 63 ), thus adding a dynamic “live” dimension to multiomics studies ( 64 ). Nondestructive trait quantification with in situ spectroscopy allows live monitoring of infection processes previously assessable only via destructive methods ( 40 , 62 , 65 ).…”

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

“…Therefore, proteomic and metabolomic research should be given due importance as they are the end products of the central dogma. If these approaches are integrated correctly at the right scale, they may reveal a multi-dimensional view of the plant diseases ( Crandall et al, 2020 ). Multi-omics technologies combined with the computational systems may identify the mimicking molecules in the host and/or pathogen triggering the plant defence systems ( Pathak et al, 2017 ).…”