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Expression et régulation épigénétique des gènes homéologues chez le blé tendre

Abstract : Within the plant kingdom, a lot of species are polyploids, meaning that they present two or more sub-genomes in the nucleus of their cells. Polyploidy confers genetic redundancy that offers a high potential of innovations and adaptations by relaxing natural selection on genic sequences. This allows faster sub and neo-functionalization of genes but also a loss of sequences that might be stochastic or not between the sub-genomes. Bread wheat is a recent polyploidy species that derived from two interspecific hybridizations that occurred 800 000 and 10 000 years ago. The genome of this species contains three sub-genomes: AABBDD and in theory three copies of each gene (1A:1B:1D). However, genomic analysis of the genome sequences reveals that half of the genes present copy number variations (NA:NB:ND). Within this scientific context, we wanted to answer questions such as: How this genetic redundancy evaluates after the polyploïdisation process? Is-it possible to observe differences in terms of gene expression that could correspond to functional evolution for this recently formed species? Which mechanisms could explain those processes? The objective of this PhD was to analyses relative expressions of homoeologous genes of bread wheat for groups presenting one copy on each sub-genomes (1 :1 :1, triades) and groups presenting a copy number variation with a loss (0:1:1, 1:0:1 ou 1:1:0), dyads or a duplication (2:1:1, 1:2:1 ou 1:1:2, tetrads) of sequences. We linked this analysis to genomic characteristics such as chromosome structure (genomic position of genes for exemple), evolution (presence or absence of lost and duplicated copies within diploid genomes of the progenitor species) and epigenetics (histone modifications). We used RNA-seq and ChIP-seq data released at the same time as the publication of the genomic reference sequence of bread wheat (IWGSC 2018). We highlight that the 51,1% of triads genes present mostly (81%) a balanced expression across the 15 tissues and developmental stages analyzed (high and constitutive expression) Those genes are mainly associated with the H3K9ac histone mark that is linked to an active transcription of genes. At the opposite, dyad genes (11,7% of High Confidence wheat genes) and tetrad genes (2,8%) present more frequently unbalanced expression patterns (36% and 74,5% respectively). Those genes are more associated with the histone mark H3K27me3 defining facultative heterochromatin and that target genes with transient expression. No dominance of one sub-genome on the others was discovered at the whole genome scale but rather stochastic suppression of genes copies. These results reveals potential sub-functionalization of genes, more frequent for copies present I the distal regions of chromosomes and associated with the epigenetic mark H3K27me3. Even if the homoeolog expression bias mostly corresponds to already existing divergence between diploid progenitor species, we nevertheless observe expression bias corresponding to the different step of bread wheat evolutive history: copies from sub-genome D are less repressed than the A or B copies; expression bias between AABB copies are more pronounced. In that respect the co-evolution of the two sub-genomes AABB during 800 000 years are traceable while D sub-genome seems to still present a nearly autonomous expression Combined together, these results suggest that wheat genome contains genes evolutionary constraints that correspond to a “core” genome of the species with basic conserved function (triad genes) and genes that present variation of the number of gene copies with differential regulations and specific functions that correspond to “dispensable” genes (dyads and tetrads).
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https://tel.archives-ouvertes.fr/tel-03144011
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Submitted on : Wednesday, February 17, 2021 - 11:25:35 AM
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Caroline Juery. Expression et régulation épigénétique des gènes homéologues chez le blé tendre. Biologie végétale. Université Clermont Auvergne, 2020. Français. ⟨NNT : 2020CLFAC037⟩. ⟨tel-03144011⟩

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