Genetic and ecophysiological bases of metabolite content involved in quality and varietal resistance

Background

Our team has demonstrated that metabolites—mainly carotenoids, polyphenols, and terpenes—play a central role both in nutritional and organoleptic quality (Perrin et al., 2017) and in plant resistance mechanisms against Alternaria dauci (Koutouan et al., 2018; Ramaroson et al., 2025).

Metabolite accumulation is strongly influenced by interactions between genotype, environment, and agricultural practices (G×E×P), making these traits complex to analyze and to breed for (Chevalier et al., 2021; 2022).

Objectives

The objectives of our research are to: 

• identify the genetic bases of these polygenic traits, 
• decipher the mechanisms controlling the biosynthesis and accumulation of these metabolites,
• better understand varietal plasticity under diverse growing conditions

Ultimately, we aim to leverage this knowledge for plant breeding applications, particularly through the identification of predictive markers of quality and resistance.

Methodologies and Approaches

To address these challenges, our team develops integrative approaches combining genetics, genomics, transcriptomics, metabolomics, and ecophysiology, applied to a wide range of genetic diversity.

Multi-environment experimental designs enable us to analyze G×E×P interactions. Approaches such as association genetics, mQTL–rQTL co-localization and functional validation tools (overexpression, gene silencing, genome editing) are implemented to confirm the role of candidate genes and metabolites.

Key Findings

Recent results highlight the structuring role of specialized metabolites in achieving dual performance in quality and resistance.

Regarding resistance to Alternaria dauci, metabolomic approaches have identified discriminant profiles between resistant and susceptible genotypes, largely dominated by flavonoids and terpenes (Koutouan et al., 2018; 2019). Integration of genetic, metabolic, and transcriptomic data has led to the identification of genomic regions where mQTLs co-localize with rQTLs, as well as candidate antifungal terpenes such as camphene, α-pinene, caryophyllene, and α-humulene (Koutouan et al., 2023).

More recently, the identification of a bHLH162 transcription factor involved in the accumulation of rutinosylated flavonoids (apigenin, luteolin, chrysoeriol) has provided a direct link between genetic regulation, metabolite accumulation, and antifungal activity (Koutouan et al., 2025). These findings open up promising perspectives for the development of metabolic and genetic markers for breeding (Ramaroson et al., 2025).

In parallel, research on nutritional quality has improved our understanding of the genetic and environmental determinants of carotenoid accumulation. Candidate gene approaches have highlighted the key role of biosynthetic pathway genes such as ZEP, phytoene desaturase, and CYP97A3 (Jourdan et al., 2015; Welsch et al., 2017). Gene expression levels are correlated with differences in accumulation between root tissues, particularly between phloem and xylem (Perrin et al., 2016).

Multi-location trials have confirmed the influence of pedoclimatic factors and agricultural practices on carotenoid and sugar contents (Chevalier et al., 2022). The Caroqual and Gesiiqua projects also revealed strong metabolite plasticity, with both genotype and environment playing structuring roles (Chevalier et al., 2021).

Finally, these results emphasize the link between metabolic profiles and health benefits, as growing conditions modulate the biological activity of carrot extracts in various cellular models (Soleti et al., 2020).

Perspectives

Future research will focus more specifically on the effect of temperature on metabolite accumulation traits. A PhD project has been submitted to the VAAME doctoral school entitled:
“Adaptive response to climate change and genetic diversity: effect of high temperatures on development and production quality in Daucus carota.”

We aim to strengthen our integrative approach by deepening the analysis of Genotype × Environment × Crop Management (G×E×C) interactions across a broader range of genotypes and environments, with a tighter integration of ecophysiology and genetics. These results will be linked to the characterization of Alternaria dauci susceptibility as a function of temperature.

The goal is to achieve sustainable dual performance, combining product quality and crop resistance.

Partnerships and Infrastructure

Our research is supported by: 

• a network of public and private partners at national and international levels through multi-year projects, 
• strong collaborations, notably with the Fungisem and Bidefi teams at IRHS, 
• the exploitation of genetic diversity from the “Carrot and Other Apiaceae” Biological Resource Center (CRB), 
• shared research facilities at IRHS, including the Phenotic platform and the technical platforms of the SFR Quasav, 
• the valuable contribution of undergraduate, Master’s, and PhD students hosted within the team.