Complementarity of Constitutive and Induced Resistance (Biocontrol) and Impacts on Quality

Background

We have demonstrated that the use of biocontrol products (bioPPPs) modulates metabolic pathways (H2020 OPTIMA project). However, since flavonoids and terpenes are also involved in the nutritional and organoleptic quality of roots, their modulation may affect not only defense processes but also product quality. This raises the question of the balance between constitutive and induced resistance and their respective impacts on harvested product quality, which we aim to address.

Objectives

Our research aims to determine to what extent constitutive and induced resistance mechanisms are complementary, and how their combination can enhance protection against Alternaria dauci. This fungal pathogen is responsible for Alternaria leaf blight, the most damaging foliar disease in carrot.

A major challenge is to identify the genetic and environmental determinants underlying varietal responsiveness to PDS, as well as the optimal conditions for the use of biocontrol products. In the longer term, the objective is to assess the impact of these strategies on root quality, in order to ensure dual performance in terms of quality and immunity.

Methodologies and Approaches

Our team develops experimental approaches combining controlled environment assays and field trials, using a wide range of contrasted genotypes. Several biocontrol products, including PDS, have been evaluated for their efficacy against A. dauci.

An original biomolecular tool based on qPFD® technology was developed to monitor the expression of defense-related genes and to characterize the induced response triggered by these products (Brisset et al., 2019; Moussa et al., 2024; Le Clerc et al., 2025). Complementary approaches (RNA-seq, qRT-PCR) are used to identify genes involved in induced resistance and to assess their modulation by environmental factors, particularly temperature.

In addition, co-localization analyses of resistance QTLs (rQTLs) and metabolite QTLs (mQTLs), along with biochemical and sensory analyses, were conducted to evaluate the impact of resistance breeding on root quality.

Key Findings

Results from the OPTIMA project showed that several bioPPPs can provide effective protection against A. dauci, although with strong dependence on genotype and environmental conditions. Higher efficacy was observed in susceptible or moderately resistant genotypes, suggesting complementarity between constitutive and induced resistance.

Analysis of defense gene expression linked the efficacy of certain products to the activation of key plant immunity pathways (PR proteins, salicylic acid pathway, oxidative stress enzymes) (Le Clerc et al., 2025).

These findings also highlight significant variability in varietal responsiveness to PDS, involving both the capacity to induce defense gene expression and the resulting level of protection. Overall, they confirm that the rational combination of genetic resistance and biocontrol represents a promising strategy for sustainable crop protection.

This work is being extended within the ALVAREX PhD project, which investigates in particular the effects of high-temperature regimes on defense induction and the efficacy of carrot protection against A. dauci.

The AlterQual project demonstrated that resistance to A. dauci can be combined with desirable organoleptic quality. Specifically, the combined analysis of resistance QTLs (rQTLs) and mQTLs associated with bitterness revealed that certain genomic regions independently regulate these traits. This opens the way for breeding strategies combining disease resistance and low bitterness, despite the presence of some unfavorable co-localization regions (Le Clerc et al., 2019).

Furthermore, our studies showed that both biotic and abiotic stresses (e.g., water stress) can strongly affect nutritional quality. In particular, infection by A. dauci can significantly reduce carotenoid content (Perrin et al., 2017).

Perspectives

Beyond plant protection, a key challenge for the team is to better understand the impact of bioPPPs and environmental conditions on root quality. As mentioned, defense induction involves metabolic reprogramming, which may alter the accumulation of metabolites contributing to nutritional and sensory quality.

Ongoing (ALVAREX PhD) and future work aims to analyze these interactions, particularly under the combined effects of temperature and PDS application. The working hypothesis is that abiotic stress may redirect plant resources at the expense of both quality and defense, while PDS could help rebalance these processes.

Identifying the underlying mechanisms will enable optimization of agronomic practices (varietal choice, timing of applications) to reconcile product quality with biocontrol efficiency.

Partnerships and Infrastructures

As with other research themes of the team, our work relies on: 

• close collaborations with international, national, and local research teams (Respom and Fungisem groups at IRHS), 
• analytical platforms of the SFR QuaSav, 
• experimental facilities including greenhouse systems (Phénotic platform), tunnels, and open-field trials.

The European OPTIMA project has established a framework for the evaluation of biocontrol solutions and their transfer to production systems.