Genetic determinism of inulin metabolism in industrial chicory (Cichorium intybus L.) : an association mapping approach

Inulin is a fructose polymer extracted from the root of industrial chicory (Cichorium intybus L.). The quality of the root extract is determined by the polymerization degree of inulin molecules and the free fructose concentration. Low autumnal temperatures trigger an inulin degradation phase which decreases the quality of the root extract. Therefore, the objective of this thesis was to understand the genetic determinism of the synthesis and the cold induced degradation of inulin. To do so, we evaluated the chicory genetic resources, conducted a candidate gene approach and a genome wide association study (GWAS). The assessment of the chicory genetic resources of the C.intybus germplasm confirmed the validity of the available classification, identified a new leaf cultivar subgroup and revealed a high genetic variability in most chicory groups. The candidate gene analysis investigated the associations between genetic polymorphisms in candidate genes involved in the inulin metabolism and the susceptibility to cold-induced inulin degradation. An indel in 1 FEH IIb was responsible for up to 35 % of the variance of traits describing the susceptibility to cold-induced inulin degradation, in a panel of 112 lines. A genome draft covering 85% of the chicory genome was created to map the SNPs identified by genotyping by sequencing in a panel of 366 lines, characterized by a very low linkage disequilibrium extent. The GWAS conducted on the panel identified, along with the 1 FEH IIb indel, new SNPs significantly associated to a small fraction of the variability of several traits describing the inulin and carbohydrates synthesis and the cold induced degradation of inulin. Therefore we concluded that the genetic determinism of inulin synthesis is multigenic and determined by several minor effect QTLs when cold induced inulin degradation result from the action of one major effect QTL and at least one minor effect QTL.
(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 2015