eQTL Analysis Elucidates the Genetic Basis Underlying Transgressive Gene Expression in Nelumbo Hybrids

Hybridization can induce transgressive gene expression, which may often contribute to hybrid vigour or dysfunction. Nevertheless, how different cis- and trans-regulatory variants between parental species influence hybrid expression novelty remains largely unknown. To decipher the detailed genetic architecture underlying this phenomenon, we performed expression quantitative trait locus (eQTL) mapping in a multi-generational Nelumbo population, including parental species (N. nucifera and N. lutea), F₁ hybrids and backcrossed F₂ (BC₁F₂) individuals. Using the Matrix eQTL under an additive linear model with covariates, our analysis identified 147,872 cis-eQTL and 151,632 trans-eQTL SNP-gene associations, which regulated the expression of 2538 cis-eGenes and 4805 trans-eGenes, respectively. Notably, trans-eQTLs exhibit significantly stronger regulatory effects on gene expression variation than cis-eQTLs. Trans-eQTLs, over-represented by transcription factors, such as C2H2, MYB, FAR1, are predominant drivers of transgressive expression in hybrids, which is markedly more prevalent in segregating BC₁F₂ individuals. We further demonstrated that cis- and trans-regulatory variants are linked to transgressive expression of crucial genes in the benzylisoquinoline alkaloid (a key medicinal metabolite of Nelumbo) biosynthetic pathway. These findings collectively highlight the primary influence of trans-regulatory rewiring on generating transgressive expression in hybrid populations. In conclusion, our study provides valuable genetic resources for understanding how regulatory network rewiring contributes to transcriptional variation and transgressive phenotypes in interspecific hybrids between species.