Complex genetic architecture of leaf shape is associated with gene expression variation in Populus tremula

Leaf shape is a defining feature of how we recognise and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. Identification of the genetic components controlling variation in such complex traits would enable future applications such as re-engineering developmental programs to maximise growth performance under different abiotic conditions. We characterised the genetic architecture of leaf shape variation in Eurasian aspen (_Populus tremula_ L.) by performing a genome wide association study (GWAS). To ascertain whether identified GWAS candidates were central within the leaf development transcriptional program, we performed gene co-expression network analyses from developmental series profiling contrasting leaf forms. We additionally performed regression analyses to identify developmental gene expression profiles predictive of physiognomy traits. We identified genes that were differentially expressed between groups of genotypes with contrasting leaf shapes from the GWAS population and examined their developmental expression profiles. These data were integrated with expression GWAS results to define a set of candidate gene associated with leaf shape variation. Our results indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not central regulators within the leaf development gene expression program and exhibited signatures of relaxed selection. Genes identified included numerous novel candidates with no known function in leaf development. These results provide targets for functional characterisation and a comprehensive resource for exploring gene expression during leaf development in aspen, available at http://aspleaf.plantgenie.org.