Bases of varietal adaptability, Environmental factors and Genotype x Environment interactions driving nutritional and organoleptic quality traits (Caroqual and Gesiiqua projects).

Within the framework of an a priori approach on the carotenoid content, the effects of several genes of the carotenoid biosynthesis pathway were investigated using a candidate gene type association genetics approach. We previously showed that, on one hand, alleles of zeaxanthin epoxidase (ZEP) and phytoene desaturase would thus be involved in the overall content of carotenoids and β-carotene, the major compound in carrots (Jourdan et al., 2015). On the other hand, alleles of LcyB would be involved in the control of lycopene content. In collaboration with the German team of R. Welsch in University of Friburg, we were able to confirm in a complementary way by association genetics on a broad genetic basis the involvement of the carotene hydroxylase gene (CYP97A3) in the determinism of the content of α-carotene, a gene whose role had been highlighted by a functional genetics approach (Welsch et al., 2017). In a without a priori approach, we constructed with the Bidefi IRHS team a transcriptomic chip based on the carrot genome, which allowed to identify complementary genes and pathways related to phloem development and sucrose accumulation (C. Champlin master thesis). We are currently developing an approach for functional validation of the identified genes by overexpression, silencing and gene editing (Crisp-Cas9). In order to implement an integrated view of carrot quality, the environment and the cropping system effects on the carotenoid content and gene expression were studied. It has been shown that the effect of climatic factors on carotenoid content in leaves and roots in relations with gene expression modification (Perrin et al., 2016), confirming ZEP gene role in carotenoid accumulation. Specific biotic and abiotic stresses (fig.1) were applied separately or in combination and a higher effect of A. dauci infection was recorded compared to water restriction, with a slightly higher effect when applied together (Perrin et al., 2017a). A differential accumulation and expression pattern in roots were observed in phloem tissues compared to xylem ones (Perrin et al., 2017b). To investigate the effect of environment, large multilocation trials and a wide set of quality traits were analysed. The objective was to identify the environmental factors most influencing the quality criteria (nutritional and sensory) and conversely the quality criteria most influenced by the environment. These results already brought the opportunity to give recommendations for the selection of carrot varieties for the quality traits (Geoffriau, 2019). Chevalier's PhD work (2017-2021) also focused on genotype-environment interaction and varietal plasticity for quality criteria (Gesiiqua project). As many specialized metabolites are involved in carrot nutritional and sensory quality, a metabolic approach was used to characterize a set of commercial varieties over three years and several environments. Seven metabolite groups were quantified: sugars, carotenoids, terpenes, phenolic compounds, phenylpropanoids and polyacetylenes. A large variation of root content was observed, in relation with variety, environment and variety by environment interaction effects in decreasing order of importance. A clear diversity structuration based on varieties was observed with a reduced number of metabolites, confirming the importance of variety effect. However, carrot varieties exhibited various levels of phenotypic plasticity across environments depending on the metabolite. More favourable environments were identified by AMMI model for some varieties and metabolites, showing variety adaptation capacity. This work already provides useful information for carrot breeding and production concerning variation for metabolites and variety plasticity levels. The identification of environmental factors influencing most the metabolite content is underway through multiple regression analyses. A balance between constitutive content and environmental sensitivity for compounds of interest must be reached to provide improved nutritional and sensory quality carrots.