Hybridization and genome doubling regularly stimulate plant diversification and speciation. Immediately following a polyploidization event, a genome suffers adjustments in organization and function at the genetic and epigenetic levels. These alterations have the potential to induce novel expression patterns, which together with permanent heterozygosity and gene redundancy, might result in significant phenotypic shifts and elevated evolutionary flexibility. Here we aim to screen genome-wide natural diversity in gene expression rates among sibling species in order to identify genes that may drive adaptation to different environments and lead to isolation. By taking advantage of the most recent advances in genomic technologies we will test the theoretical predictions that only a few genetic loci controlling key traits are necessary for rapid ecological diversification. We will use ecologically divergent but related species of Dactylorhiza in their native environmental context as model system. Using previously available parental reference transcriptomes, we will map millions of short reads quantitatively sequenced for several individuals with Illumina. Further, we will look for quantitative patterns correlated with native environmental parameters, as well as loci showing greater between-species expression difference relative to within-species variation. These loci will be further analyzed and their variation characterized, including across transplants. The project will lead to an enhanced appreciation of the effects of polyploidy on the evolution of metabolic pathways that are significant to adaptation and speciation. Finally, it has the potential to provide a drastically new perspective on the links between polyploidy and functional diversity and it will contribute toward a better understanding and hence prediction of the spectrum of genetic and epigenetic mechanisms active at the intraspecific (population) level.
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