Many studies have highlighted the complex, multigenic basis for heterosis (hybrid vigor) in inbred crops. Despite the lack a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, outcrossing, heterozygous, and often polyploid species, such as willow (<
em>
Salix<
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). Shrub willow is a dedicated energy crop and is bred to be fast-growing and high-yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploid progeny produced from crosses between diploid and tetraploid species. Critical in understanding heterosis, the heritability of gene expression is dependent on allele-specific expression by local and remote factors in the genome. Here, we tested whether differentially expressed genes are responsible for heterosis in triploid crosses made between diploid <
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S. purpurea<
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, diploid <
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S. viminalis<
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, and tetraploid <
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S. miyabeana<
/em>
parents. Three biological replicates of progeny and parent shoot tips were collected after 11 weeks in the greenhouse and individually sequenced via RNA-Seq (2�101). Our results highlight regulatory factors influencing differential expression and top modules of co-expressed genes correlated with heterosis for phenotypes collected in the greenhouse and in the field. We also show in diploid F<
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1<
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and F<
sub>
2<
/sub>
<
em>
S. purpurea<
/em>
that expression-level dominance and sex dimorphic expression is pervasive in shoot tips. Gene expression in triploids largely matches expected dosage values, but there are interesting categories of genes whose expression is divergent from expected dosage of alleles. Candidate genes have been identified whose differential expression be confirmed via allele-specific assays. Altogether, 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.