Most of the molecular mechanisms underlying plant partial resistance QTLs are still unknown. Two
competing hypothesis are generally invoked to link observed field resistance with actual molecular
gene function. An older hypothesis links partial resistance QTLs with overcome typical R genes
encoding classical NBS-LRR or LRR-TM type proteins. In a recent paper (Hu et al., 2008), partial plant
resistance was linked with defense mechanisms. These results led us to develop a candidate gene
approach to study partial plant resistance of carrot (Daucus carota) towards its main foliar fungal
pathogen, Alternaria dauci. Since carrot is a non-model plant, little sequence data is available on
public databases. We thus chose to develop a homology-based cloning strategy in order to detect
and sequence defense-related genes in carrot. Since A. dauci is a necrotrophic pathogen, we focused
this strategy on Jasmonic acid (JA) signaling pathway and JA controlled defense genes (such as JAZ3
or PR4). Since the degenerate primer strategy is not known to be effective on each and every gene,
we chose to apply it in a parallel fashion on a rather large set of genes. Alignments of sequence data
from eight already sequenced dicotyledonous plant species were performed for 15 genes.
Degenerate primers were defined for 10 genes involved in this JA pathway. Additionally, we defined
degenerate primers for two defense genes that are not mainly JA- regulated: the SA-regulated
defense gene PR1, and the non host defense gene PAL1. Five out of 12 genes were partially cloned
and sequenced. Two strategies are currently deployed to link these defense related genes with
partial resistance QTLs observed in the carrot-A. dauci interaction (Le Clerc et al., 2009). SNPs are
being found between the resistant and susceptible parents of our mapping populations. They will
help us to find potential QTL-candidate co-localizations. Absence of such a co-localization does not
mean that a potential candidate is not involved in defense. It is also possible that the QTL influences
defense-related genes activation rather than the efficiency of the cognate PR proteins. For this
reason, we also plan to study the induction of these genes by A. dauci in both susceptible and
resistant backgrounds.