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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

A chicory genetic map of 1208 cM has been created using 247 F2 plants and 237 markers (170 AFLP, 28 SSR, 27 EST-SNP and 12 EST-SSR). This map covers 84% of the chicory genome. The chicory-genic-markers-associated sequences were used to find potential orthologs in mapped lettuce ESTs from the Compositae Genome Project Database. Twenty-seven putative orthologous pairs were retained, pinpointing seven putative blocks of synteny that covered 11% of the chicory genome and 13% of the lettuce genome, opening new perspectives for the analysis of these two species. © 2013 Blackwell Verlag GmbH.

Beta vulgaris is a biennial plant, which under both vernalization and long photoperiods, shows early flowering during the first growing year. Early flowering of sugar beet results in a reduction of sugar yields. Despite systematic phenotypic counter-selection, early flowering plants are still observed in the fields. The aim of this work was to identify sequence polymorphisms statistically associated with early flowering in sugar beet so they can be used to develop new molecular markers. These markers would contribute to improve breeding and selection for sugar beet varieties more resistant to early flowering. To reach this goal, we followed a candidate gene approach relying on the extensive knowledge of flowering time control available on the model species Arabidopsis thaliana. In our strategy, we first isolated homologous genes related to flowering time control in sugar beet, we then studied their polymorphisms by performing EcoTILLING in contrasted samples originating from the same cultivar (Angeliqua). We finally looked for putative association between the identified genetic polymorphisms and the early flowering phenotype. At the end of this research, we were able to identify SNP and indel polymorphisms in BvGI, BvSUF4, BvPHYB, BvPHYA, BvFT1, BvCRY1, BvFY and BvTINYL2 genes. Following the genotyping of two sets of contrasted sugar beet plants with PAMSA probes, statistically significant associations were confirmed between detected polymorphisms within BvGI, BvSUF4, BvPHYB, BvTINYL2 genes and the early flowering phenotype. In conclusion, the candidate gene approach proved to be a promising method to investigate phenotype / genotype association in sugar beet. Four promising targets were identified in this study. These results might favor the development of improved varieties of sugar beet., (DOCSC03) -- FUNDP, 2014

n/a, n/a, (DOCSC03) -- FUNDP, 2012

Belgium is the world's largest producer of industrial chicory. This species is cultivated to extract inulin, a storage polysaccharide with pre-biotic properties used in food processing. The selection of chicory varieties is mainly phenotypic and based essentially on sugar yield, bolting, disease resistance and root morphology. The objective of this work is to develop molecular tools that can improve and facilitate breeding. EST (Expressed Sequence Tag) libraries were used to develop SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) genic markers. A total of 130 markers were validated for industrial chicory. These markers were used to build a genetic map of 1208 cM composed of 237 markers (152 AFLP markers, 27 SNP markers and 40 SSR markers) in collaboration with UCL and the Chicoline Company. The transcribed sequences associated with mapped genic markers were then used to search for orthologs in lettuce to develop a comparative map between the two species. This analysis has allowed identifying regions of synteny in which there were positional candidate genes potentially involved in different mechanisms of interest for the selection of chicory., La Belgique est le premier producteur mondial de chicorée industrielle. Cette espèce est cultivée afin d’en extraire l’inuline, un polysaccharide de réserve utilisé dans l’agro-alimentaire et aux vertus pré-biotiques. La sélection des variétés cultivées de chicorée est majoritairement phénotypique et basée essentiellement sur le rendement en sucre, la montaison, la résistance aux maladies ainsi que sur la morphologie racinaire. L’objectif de ce travail consiste à développer des outils moléculaires pouvant améliorer et faciliter cette sélection. Les banques EST (Expressed Sequence Tag) ont été utilisées afin de développer des marqueurs géniques de type SSR (Simple Sequence Repeats) et SNP (Single Nucleotide Polymorphism). Au total, 130 marqueurs ont été validés chez la chicorée industrielle. Ces marqueurs ont été utilisés pour la construction d’une carte génétique de 1208 cM composée de 237 marqueurs (152 marqueurs AFLP, 27 marqueurs SNP et 40 marqueurs SSR) en collaboration avec l’UCL et la société Chicoline. Les séquences transcrites associées aux marqueurs géniques cartographiés ont ensuite été utilisées pour la recherche d’orthologues chez la laitue afin d’élaborer une carte comparative entre les deux espèces. Cette analyse a permis de mettre en évidence des régions de synténie dans lesquelles se trouvaient des gènes candidats positionnels potentiellement impliqués dans divers mécanismes d’intérêt pour la sélection de la chicorée., (DOCSC03) -- FUNDP, 2012

Chicory (Cichorium intybus) roots contain high amounts of inulin, a fructose polymer used as a storage carbohydrate by the plant and as a human dietary and prebiotic compound. We performed 2-D electrophoretic analysis of proteins from root material before the first freezing period. The proteins were digested with trypsin and the peptides analyzed by MS (MALDI-TOF/TOF). From the 881 protein spots analyzed, 714 proteins corresponded to a database accession, 619 of which were classified into functional categories. Besides expected proteins (e.g. related to metabolism, energy, protein synthesis, or cell structure), other well-represented categories were proteins related to folding and stability (49 spots), proteolysis (49 spots), and the stress response (67 spots). The importance of abiotic stress response was confirmed by the observation that 7 of the 21 most intense protein spots are known to be involved in cold acclimation. These results suggest a major effect of the low temperature period that preceded root harvesting.

Background The industrial chicory, Cichorium intybus, is a member of the Asteraceae family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison. Results Approximately 1,000 Expressed Sequence Tags (EST) were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution. Conclusion This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.

Biodiversity used within the context of plant enhancement presupposes an analysis of the locally existing genotypes adapted to particular environments. Within the scope of a pigeon pea enhancement project, we carried out the exploration and collection of pigeon pea landraces from Lambayeque, department located at the north of Peru. Then, we proceeded to the agro-morphological characterization of the maternal families (derived from these landraces) based on descriptors. At the same time, we undertook the molecular characterization of the collection, as well as in some Indian and African accessions, by using microsatellites markers developed by us. We also used microsatellites provided by the ICRISAT. The molecular characterization is an important stage, which requires low-cost precision instruments, efficient and easy to use. One of them are the microsatellites, codominant markers. Thanks to these seven microsatellite markers, we made evident the diversity inside the collection and the proximity between the Peruvian and the African groups. Using molecular techniques such as the microsatellites is important as they are supplementary to that of the descriptors. Besides, they play an essential role in the assessment of promising crops in countries like Peru., L’utilisation de la biodiversité dans le cadre de l’amélioration végétale présuppose une analyse des génotypes existants localement et adaptés à des environnements particuliers. Dans le cadre d’un projet d’amélioration du pois d’Angola ou pigeonpea, nous avons réalisé la prospection et la collecte de landraces du pigeonpea à Lambayeque, département au nord du Pérou. Par la suite, nous avons procédé à la caractérisation agro-morphologique des familles maternelles (issues de ces landraces) sur base des descripteurs. Parallèlement, nous avons effectué la caractérisation moléculaire de la collection ainsi que celles de certaines accessions indiennes et africaines à l’aide de marqueurs microsatellites que nous avons développés. Nous avons également utilisé des microsatellites fournis par l’ICRISAT. La caractérisation moléculaire est une étape importante, elle nécessite des outils précis, au coût peu élevé, performants et facilement utilisables. Un de ceux-ci : les microsatellites, marqueurs co-dominants. Grâce à ces sept marqueurs microsatellites, nous avons pu mettre en évidence la diversité au sein de la collection ainsi que le rapprochement entre le pool péruvien et africain. L’utilisation des techniques moléculaires comme les microsatellites s’avère importante car elle est complémentaire à celle des descripteurs. D’ailleurs son rôle est essentiel dans la valorisation des cultures d’avenir dans des pays comme le Pérou., (DOCSC03 ) -- FUNDP, 2009