Transcriptome Variation in Shrub Willow (Salix) Hybrids

Interspecific hybridization has been a primary approach in breeding shrub willow (Salix spp.) as an energy crop, as hybrids often display heterosis for yield. Expanding available genomic resources for shrub willow will not only facilitate breeding efforts but also contribute to our understanding of hybrid vigor in outcrossing woody perennials. Utilizing RNA-Seq, transcriptome variation in hybrids of intra- and interspecific crosses of shrub willow is being investigated to determine genome-wide dosage-dependent allelic bias and differential patterns of cis- and trans-regulation within and between hybrid categories. Shoot-tip and stem internode libraries of 10 random progeny from  intra- and interspecific families and their parents (S. purpurea [2X], S. viminalis [2X], and S. miyabeana [4X]) have been sequenced and mapped to reference assemblies to identify alleles that correlate with heterosis for biomass yield and variation in lignocellulosic composition. Although gene expression within a hybrid family is predicted to be uniform, conservative results from an intraspecific S. purpurea F₁ family indicate extensive non-additive gene expression (~440 DE; FDR <0.05; >2 logFC) in progeny compared to mid-parent transcript abundance. Transcription factors account for a majority of these differences and among those most significant are down-regulated in hybrid progeny. However, when only shoot-tip samples of hybrid progeny are considered, transcript variation manifests a well-defined structure correlated with gender, providing useful insight to the contrasting factors controlling stem and shoot development. Allele-specific expression will be confirmed using validation assays and will consequently be used as a resource for developing predictive models for heterosis in hybrid shrub willow.