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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu INRA Clermont Auvergne University


Joint Research Unit 1095 Genetics, Diversity and Ecophysiology of Cereals

2. Gene space analyses

Objective : Deciphering the organization and evolution of the gene space, and the relationships between genome structure and expression

Access to the sequence of chromosome 3B enables structural and


functional analyses to adress different fundamental questions. These analyses are organised into four main sections:

1. Identification of the non-repeated fraction of chromosome 3B.

The genomic sequences produced in the 3BSEQ project are analysed using bioinformatics tools developed in the laboratory by F. Choulet and P. Leroy. In particular, the use of an Mathematically Defined Repeat (MDR) index permits the ab initio annotation of repeated sequences and the development of a catalogue of low copy number sequences (genes and surrounding regions) that will used in subsequent analyses. The rest of the sequence that comprises essentially the repeated and non coding fractions of the genome is analysed to provide an exhaustive list of Transposable Elements and complete the data obtained in pilot projects.

2. Detailed transcriptional mapping and functional annotation of chromosome 3B.

Access to the sequence of chromosome 3B allows us to construct its detailed transcriptional map and thus establish the expression profiles of all the genes identified throughout the chromosome, by combining different transcriptomic approaches (hybridisations on a DNA chip, RNA-Seq., etc.). We would like to link the expression of genes with their structural context. In addition, we will be able to identify new transcriptional units, genes, conserved non-coding sequences or cis-natural anti-sense transcripts (cis-NAT), miRNA, chimeric transcripts between genes and transposable elements, etc., in regions previously annotated as intergenic, and thus complete the functional annotation of the chromosome.

3. Study of variations in gene content.

In a neoformed polyploid, an increase in gene dosage causes genomic instabilities that must be compensated for in order to ensure the viability of the newly-created species. Stabilisation is often accompanied by epigenetic and genetic modifications. The latter may be characterised by chromosomal rearrangements, and notably by the deletion of duplicated genes. This mechanism for gene suppression/addition, known as copy number variations (CNVs), or presence-absence variations (PAVs), has been shown in other species (human, maize) to play a major role in the establishment of intraspecific variability, in genome plasticity and species adaptation. In hexaploid wheat, CNVs and PAVs may appear between homoeologous genomes and thus characterise a phenomenon of genetic diploidisation through a loss of genes, but also between different varieties, where they may be involved in specific adaptation. Based on homoeologous group 3 chromosomes in the first instance, and then by extending these analyses to other chromosomes as international programmes advance, we thus propose to study the effects of polyploidisation on gene content (gene loss, transposition, duplications, etc.) and the impact of CNVs and PAVs as drivers of diversity in wheat.

4. Exploration of epigenetic regulations in wheat.

As mentioned above, polyploidisation is often accompanied by epigenetic modifications that can ensure a rapid regulation of the expression of new homoeologous genes. These modifications mainly concern the methylation of DNA and the modification of histones (acetylation, methylation, etc.) which lead in turn to modifications of the chromatin structure (euchromatin vs. heterochromatin) and of gene expression. In wheat, very little is known to date about the epigenetic landscape, mainly because of a lack of genomic sequences to perform this type of analysis. Access to the sequence of chromosome 3B offers a unique opportunity to explore what might be one of the principal mechanisms regulating gene expression in such a polyploid species. To initiate this work, a local partnership is currently being set up with the GReD group at the University of Clermont-Ferrand who are specialised in epigenetic studies in drosophila and A. thaliana.