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

Dernière mise à jour : Mai 2018

Menu INRA Clermont Auvergne University

UMR GDEC

Joint Research Unit 1095 Genetics, Diversity and Ecophysiology of Cereals

1. Sequencing the wheat genome

Aim: Producing a reference sequence of the bread wheat genome

Bread wheat is the last major crop for which there is no reference genome sequence publicly available, although draft assemblies are now available for the hexaploid bread wheat genome and also for diploid relatives (IWGSC 2014; Chapman et al. 2015; Brenchley et al., 2012; Jia et al., 2013; Ling et al., 2013). Obtaining a high quality reference sequence is, however, of major interest, as demonstrated in rice for instance, with the development of markers, functional genomics platforms, and the cloning of genes controlling the main traits (Hao and Lin, 2010; Jiang et al., 2012).

sequence_black

Genome complexity is the main limiting factor for getting a high quality reference sequence of the wheat genome. A solution is to reduce this complexity using flow sorting of the individual chromosomes or chromosome arms. This allows overcoming the main problems due to repeated DNA, especially due to polyploidy that is, the presence of three highly similar homeologous genomes in the same nucleus. 

The GDEC institute has pioneered the chromosome-specific approach by using chromosome 3B (900 Mb; more than two times larger than the rice genome) as a model. After the completion of the physical map of wheat chromosome 3B (Paux et al. 2008), we produced and recently published the first reference sequence of this giant wheat chromosome in the framework of the 3BSEQ project (founded by the ANR and FranceAgrimer) in collaboration with ou partners, especially from the Genoscope and INRA-URGI. Combination of multiple sequencing data has allowed us to assemble a reference sequence (called "pseudomolecule") of chromosome 3B representing 774 Mb, une world-wide first (Choulet et al. Science 2014).

We also developed bioinformatics tools dedicated to sequence analyse, of which the TriAnnot pipeline used for calling genes and transposable elements in the genomic sequences. Analyses revealed main relationships between genome structure, meiotic recombinaison,  gene expression, evolution of the gene content (especially gene duplications) and  dynamics of transposable elements.

The team SEVEN is an active member of the International Wheat Genome Sequencing Consortium (IWGSC). In parallel to our work on 3B, we were part of the international effort to produce and publish draft assemblies of the 21 wheat chromosomes (IWGSC Science 2014).

Project

The IWGSC aims at producing a reference sequence for the 20 remaining chromosomes. This was defined as a priority by the G20 Agriculture Ministries (see the Wheat Initiative). Therefore, the IWGSC has elaborated a project to meet this challenge within 3 years. Our group is identified as a key laboratory for sequence assembly, anchoring and annotation. Thanks to the INRA and in the framework of the WheatSeq project ("France Génomique"), our group, together with our collaborators at Genoscope, INRA CNRGV, Dolezel's lab (IEB, Czech Republic), Korol's lab (The Institute of Evolution, Israel) and Bayer CropScience, started the sequencing of 2 other chromosomes: 1B and 4B. The analyses that were performed on 3B will be extended to these 2 chromosomes and to the entire genome as far as the reference sequences will be publicly available.