Regulatory architecture and variation of gene expression in wild and domesticated barley

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Intraspecific variation of gene expression regulation in crop plants has been implicated in both domestication and adaptation to stress conditions. The recent advances in cereal genomics have enabled the genome-wide quantification of gene expression and the dissection of gene regulatory variation in diverse germplasm collections. The proposed research aims at ascertaining (i) whether barley domestication has been accompanied by a loss of regulatory variation and (ii) whether this entailed a concomitant reduction of variability in response to environmental perturbations. We will use high-throughput sequencing to quantify allele-specific expression in seedling tissue of four domesticated and four wild genotypes of barley and their F1 hybrids with a reference genotype to investigate to what extent domestication has reshaped the transcriptome of barley and how patterns of regulatory variation differ between wild and domesticated barley. We will also enquire into how abiotic stress modulates the regulation of gene expression in domesticated and wild barley by comparing expression data from seedlings grown under cold stress and control conditions. Our results will shed light at a genome-wide level on the relative contribution of cis- and trans-effects to gene regulation in barley, the inheritance of gene expression and their relation to genetic diversity and genome evolution. An improved understanding of the regulatory architecture of gene expression will contribute to the informed utilization of wild germplasm in crop improvement and to elucidating the molecular basis of heterosis in barley.