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Abstract

One of the central goals in evolutionary genetics is to understand how the distinct allelic variants can shape phenotypic diversity, either across environments or in an environment-specific manner. Genome- wide association studies (GWAS) and linkage mapping strategies have identified countless numbers of QTLs in plants; from these, however, only a small number of essentially large-effect loci have been molecularly characterised. Moreover, many of them have identified changes that dramatically alter the encoded protein sequence. Here, we measure the effects of non-coding changes by estimating genome- wide levels of allele-specific expression (ASE) in A. thaliana Col x Cvi F1 hybrid individuals (a robust test for cis-acting regulation). Furthermore, in order to account for genetic (trans-effect) and environmental interactions, hybrids and parental accessions were grown under well-watered and water-deficit conditions, as contrasting treatments. Subsequently, we developed a model to estimate the contribution of the genotype, the environment and their interactions, on the final gene expression levels. In this way, we are now able to isolate the effect of each component and identify genes exhibiting ASE and distinct environmental responses. We revealed that, in this cross and in the non-stress environment, more than 30% of expressed genes show detectable levels of significant cis-regulatory variation, whilst 15% show signatures of being trans-regulated. We found strong correlation between conditions for genes being regulated in cis, demonstrating the robust nature of local variation towards environmental perturbation. On the contrary, a higher number of genes were trans-regulated under water-deficit, likely due to a stress-specific response in pathways associated to drought. Identification of regulatory gene networks and accession-specific responses, represents an important step towards bridging the gap between non-coding changes and natural phenotypic variation.