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The loss of mini-exon 2 in the 1-FEH IIb glycosyl-hydrolase results in a putative non-functional allele. This loss of function has a strong impact on the susceptibility to post-harvest inulin depolymerization. Significant variation of copy number was identified in its close paralog 1-FEH IIa, but no quantitative effect of copy number on carbohydrates-related phenotypes was detected. Inulin polyfructan is the second most abundant storage carbohydrate in flowering plants. After harvest, it is depolymerized by fructan exohydrolases (FEHs) as an adaptive response to end-season cold temperatures. In chicory, the intensity of this depolymerization differs between cultivars but also between individuals within a cultivar. Regarding this phenotypic variability, we recently identified statistically significant associations between inulin degradation and genetic polymorphisms located in three FEHs. We present here new results of a systematic analysis of copy number variation (CNV) in five key members of the chicory (Cichorium intybus) GH32 multigenic family, including three FEH genes and the two inulin biosynthesis genes: 1-SST and 1-FFT. qPCR analysis identified a significant variability of relative copy number only in the 1-FEH IIa gene. However, this CNV had no quantitative effect. Instead, cloning of the full length gDNA of a close paralogous sequence (1-FEH IIb) identified a 1028 bp deletion in lines less susceptible to post-harvest inulin depolymerization. This region comprises a 9 bp mini-exon containing one of the three conserved residues of the active site. This results in a putative non-functional 1-FEH IIb allele and an observed lower inulin depolymerization. Extensive genotyping confirmed that the loss of mini-exon 2 in 1-FEH IIb and the previously identified 47 bp duplication located in the 3′UTR of 1-FEH IIa belong to a single haplotype, both being statistically associated with reduced susceptibility to post-harvest inulin depolymerization. Emergence of these hap

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