Functional diversity and novelty with varying ploidy in wheat

In the natural allohexaploid wheat T. aestivum (AABBDD), three divergent wheat genomes became ‘coresident’ in a single nucleus, through two successive allopolyploidization events. This wheat allohexaploid is relatively genetically stability as we have recently shown. The objective now is to understand reprogramming of gene expression with varying ploidy in wheat, by characterizing both natural and synthetic allopolyploids. Genome-wide analysis of gene expression using µarray showed that majority of transcripts (98.7%) exhibit same expression levels when comparing natural wheat allohexaploids and allotetraploids, suggesting important compensation between the constitutant homoeoalleles. Moreover, our analysis showed that majority of genes, which expression was different between the natural wheat allohexaploids and allotetraploids, adopt in the synthetic allohexaploids expression levels which were similar to those observed in the natural allohexaploids. Such comparison suggests thus that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations. We also focused on understanding homoeoallele contribution and compensation to the global gene expression, as well as their possible neo- and subfunctionalization. As a pilot case of study, we recently investigated the organization,evolution, and function of homoeoalleles of the important Q/q gene, known to have played a major role in domestication of polyploid wheat. Combined phenotypic and expression analysis indicated that, the evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of one homoeoallele (5AQ), a pseudogenization of a second homoeoallele (5Bq) that became non-protein coding RNA (npcRNA) but remains functional as affecting phenotype and expression of the other homoeoalleles, and a subfunctionalization of the third copy (5Dq), all contributing to the domestication traits. They interacts and crosstalk to each others, probably via epigenetic regulation. We have now undertook genomewide characterization of gene expression regulation using next generation Solexa HighSeq technology with the objective of distinguishing majority of the homoeoallele expression. The role of functional regulation as well as that of compensation, neo- and the sub-functionalization of homoeoalleles in the overall stabilization of wheat allopolyploids will be discussed.