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

Dernière mise à jour : Mai 2018

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Joint Research Unit 1095 Genetics, Diversity and Ecophysiology of Cereals

Lise Pingault

2014 Oct - Structural and functional analyses of the gene space of the hexaploid wheat chromosome 3B

Genome-wide studies of the bread wheat are a complicated task due to its large size (17 Gb), its allohexaploidy and its high content in repeat sequences (>80%). Using a chromosome-specific approach, the chromosome 3B (995 Mb) was successfully isolated and sequenced leading to the assembly of one pseudomolecule. The work presented in this thesis investigated the impact of the 3B chromosome size on the gene space organization. Production of transcriptomic data was achieved using RNA-Seq approach. The chromosome 3B was annotated and we predicted 7 264 features, including 5 326 full genes and 1 938 pseudogenes. We constructed RNA-Seq libraries for 15 developmental wheat conditions. Using this data we detected expression of 71.4% of the predictions, and 3 692 novel transcribed regions (NTR). We also detected alternative transcripts for 61% of the expressed genes, with 5.8 isoforms on average for one gene. Using these transcriptional data, we highlighted a partitioning of the chromosome 3B gene space. Indeed, transcription was found all along the chromosome, but genes were organized according to an increasing density gradient along the centromere-telomere axis. Based on recombination profile, we segmented the chromosome in 3 major regions: R1, R2 and R3. The region R2 was identified with low or no recombination rate corresponding to the centromeric and peri-centromeric regions (647 Mb). The regions R1 and R3 were associated with a higher recombination rate, both localized on the distal part of the short arm (58 Mb) and the long arm (69 Mb) respectively, where the recombination rate is higher. All three regions showed distinct level and specificity of gene expression as well as unique gene structure (variation size, exon number, intron size). Indeed, genes expressed in a specific condition and with a small number of alternatives transcripts were localized on regions R1 and R3. We showed that two evolutionary model could explain the link between gene structure and the level/specificity of expression : “selection for economy” and “genome design”. In conclusion, a transcriptomic studies was achieved along the 3B chromosome for the first time.
This study demonstrated a relationship between gene characteristics (structure, expression level, expression specificity and evolution) and the chromosome 3B organization. Future pseudomolecule assemblies will help us to assess the structural organization of these chromosomes. In order to better understand the cellular mechanisms of gene expression, an epigenomic study of the 3B chromosome was started.

Key words: wheat, gene space, RNA-Seq, expression, genome structure