# When Metabolomics Meets Quantitative Genetics: An Integrative Strategy to Elucidate Plant Resistance Mechanisms

## TL;DR

This paper proposes combining metabolomics and genetics to better understand how plants resist pests and diseases, improving crop breeding strategies.

## Contribution

The novel approach integrates metabolic QTLs with resistance QTLs to uncover plant defense mechanisms.

## Key findings

- Metabolic QTL mapping in segregating populations can identify genomic co-localizations with resistance QTLs.
- This integrative strategy reveals candidate genes and metabolites linked to plant resistance.
- The method refines hypotheses about the mode of action of resistance QTLs.

## Abstract

Gene pyramiding in crop varieties offers a promising strategy to achieve sustainable production and reduce reliance on pesticides. However, stacking resistance genes without understanding their biological functions may result in transient protection. Although numerous studies have mapped loci associated with resistance to biotic stresses, the underlying molecular mechanisms remain poorly characterised. Resistance genes are often involved in pest/pathogen recognition, whereas quantitative trait loci (QTLs) may act in other steps of plant immunity such as signalling and defence pathways. In parallel, specialised metabolites have attracted growing attention as key defence components, acting as antimicrobial or repellent agents. While both fields encounter challenges to precisely decipher plant defence mechanisms, making use of metabolomics on segregating populations could bypass some of these limitations. In this review, we introduce an approach based on the identification of metabolic QTLs within populations where resistance QTLs segregate, enabling the detection of genomic co‐localisations between both types of QTLs. This integrative framework can reveal specific metabolic signatures associated with resistance, thus refining hypotheses on the mode of action of resistance QTLs. Ultimately, elucidating the genetic architecture of specialised metabolism in relation to quantitative resistance will inform on more effective combinations of defence mechanisms for breeding resistant varieties.

This review presents an approach using metabolic QTL mapping in populations segregating for resistance QTLs in order to identify genomic co‐localisations.

This review presents an approach using metabolic QTL mapping in populations segregating for resistance QTLs in order to identify genomic co‐localisations.

This strategy helps highlight specific candidate genes and metabolites and refine hypotheses on the mode of action of resistance QTLs

This strategy helps highlight specific candidate genes and metabolites and refine hypotheses on the mode of action of resistance QTLs