Differential Expression, Regulatory Divergence, and Sex Dimorphism Pervade the Shrub Willow (Salix spp.) Transcriptome

Recent genomic advances have provided the biomass feedstock community with new tools to improve traits related to biomass yield and wood chemical composition. In Salix, hybrid vigor is apparent in interspecific crosses and tends to be more pronounced in triploid progeny derived from the hybridization of tetraploid and diploid parents. Progeny and parents of full-sib intra- and interspecific F₁ and F₂ shrub willow families have been examined in order to define the basic architectures and inheritance patterns of transcriptome-wide expression. Our main objectives of this study were (1) to test for differential expression among segregating diploid, triploid, and tetraploid families with regards to contrasting sex, tissue type, and midparent expression, (2) to categorize transgressive gene expression into modes of inheritance, (3) to assess the magnitude of regulatory divergent expression, and (4) to correlate modules of co-expressed genes in parents and progeny with traits important for biomass yield. We show allele-specific expression is largely conserved in intraspecific families and highly divergent in interspecific families. Akin to the heterosis observed in the field, as the complexity of the cross increases, regulatory divergent expression increases. In addition, we utilize a full-sib F₂ S. purpurea mapping population, planted in a replicated field trial, to supplement expression work. Candidate genes that have been or have yet to be identified will be confirmed via allele-specific assays. These data will be used to develop predictive models of heterosis and complement the growing genomic resources available for the improvement of shrub willow bioenergy crops.