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UMR GDEC

Joint Research Unit 1095 Genetics, Diversity and Ecophysiology of Cereals

Task 3 : Regulation

Principle : Immediate and massive neo-/sub-functionalization of duplicated genes.

To study the impact of ancient and recent genome duplications onto gene expression, we have performed transcriptomic analyses in rice and wheat respectively. The rice genome is a good model to study the effect of paleoduplications on gene expression and based on an oligoarray of ~61,000 genes, we were able to make an inventory of genes differentially expressed in the roots, leaves and grain tissues. These data enabled us to develop an expression map of the rice genome which did not indicate any co-regulation island, i.e. a region of the genome where the genes are preferentially expressed under the same condition or the same tissue. It appears that if we compare the current gene content of the paleoduplicated fragments, only 12.6% remain still duplicated today. This allowed us to conclude that, on a time scale of about 50 to 70 million years, 87.4% of paralogous genes have been lost through pseudogenisation mechanisms affecting one of the duplicates. By studying the expression profiles of 1440 paralogs that have been retained intact in their structure, we have shown that 88%, 89%, 96% of duplicated genes no longer have the same expression profiles in grains, leaves or roots, respectively, which is indicative of a neo- or sub-functionalisation phenomenon of the duplicates.

Bread wheat appears to be a very pertinent model to compare, at different evolutionary time scales, the impact of genome doubling on gene expression for both ancient events (50-70 million years for paleoduplications) or more recent events (2.5 million years for neoduplications linked to the hexaploid nature of bread wheat) of polyploidisation. The bread wheat genome appeared nearly complete diploidized over few million years of evolution. In the bread wheat genome, deriving from the hybridization of 3 (A, B and D) progenitors, we observed that among the 19149 (20% of 99386 annotated genes) genes conserved in triplets (i.e. 6383 triplets A-B-D), only 632 (10%) triplets show the same expression profile (during the grain development). After 2.5 million years of evolution, we detected only 20% of structural redundancy (retention of A-B-D triplets) for which only 10% show a perfect expressional redundancy (expression of A-B-D triplets).

Regulation

Impact of polyploidization on gene expression (Throude et al. 2009) - The figure illustrates the duplicated genes in rice with the 12 chromosomes shown as circle and duplicated genes connected by lines in the center of the circle (left). Some expression patterns of duplicated genes during the grain development are shown in the same graph (y-axis for the level of expression and the x-axis for the grain development stages).