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No major R gene has ever been discovered. Only QTLs have been previously highlighted (Le Clerc et al., 2015a) which is interesting for putative durability of resistance but makes breeding actions more difficult and time-consuming. Deep knowledge about resistance mechanisms and decision-making tools to support breeder efforts are therefore important. For many years, our team has been working with Fungisem team to characterize the carrot/A. dauci interaction (Le Clerc et al., 2015b; Lecomte et al., 2017; Courtial et al., 2018) and to understand the resistance mechanisms involved.
Deciphering fungus toxicity allowed us to describe a new polyketide phytotoxin, aldaulactone, to show its link with Alternaria dauci aggressiveness and to highlight its role in carrot cell death or resistance depending on genotype resistance (Courtial et al., 2018; see also Fungisem team results).
Various sources of resistance were evaluated to maximize the chances of identifying potentially complementary resistance factors and to allow the ultimate combination of factors with different modes of action against the pathogen. Some resistance QTL (rQTL) have been identified in different segregating populations. Using a without a priori approach the metabolic response of the carrot to infection by the pathogen has been studied in four genotypes. In collaboration with the research unit SVQV - Université de Strasbourg - INRA Colmar, the contents of fourteen phenylpropanoid derivatives have been found to be highly discriminatory between these four resistant and susceptible genotypes (Koutouan et al., 2018). Thereafter, a metabolic phenotyping and a mQTL*-rQTL co-location approach was implemented on two segregating populations with a correlation test between resistance level and metabolite content in segregating progenies. On this basis, nine flavonoids and particularly three of them (apigenin 7-O-rutinoside, chrysoeriol 7-O-rutinoside, and luteolin 7-O-rutinoside) and seven terpenes (camphene, α-pinene, α-bisabolene, β-cubebene, caryophyllene, germacrene D and α-humulene) have been proposed as candidates to explain the mechanisms underlying some rQTL.
Using a transcriptomic microarray chip approach, some candidate genes encoding transcription factors bHLH, a UDP-glucosyltransferase and terpene synthases were identified as differentially expressed between the resistant and the susceptible genotypes and co localising with r and m QTL. These candidate genes could be linked to the accumulation of these candidate metabolites and, by domino effect, to resistance. A quantification of these metabolites within inoculated and non-inoculated plants of parental genotypes, clearly indicated that the metabolites are mainly constitutive, i.e. accumulated even in absence of the fungus.
Functional validation of candidate genes and biological effect of candidate metabolites are now under investigation to further characterise these different mechanisms of resistance.
*mQTL: metabolite QTL