Abstract: <\/strong>Genome-scale studies have revealed divergent mRNA splicing patterns between closely related species or populations. However, it is unclear whether splicing differentiation is a simple byproduct of population divergence, or whether it also acts as a mechanism for reproductive isolation. We examined mRNA splicing in wild \u00d7\u00d7 domesticated sunflower hybrids and observed 45 novel splice forms that were not found in the wild or domesticated parents, in addition to 16 high-expression parental splice forms that were absent in one or more hybrids. We identify loci associated with variation in the levels of these splice forms, finding that many aberrant transcripts were regulated by multiple alleles with nonadditive interactions. We identified particular spliceosome components that were associated with 21 aberrant isoforms, more than half of which were located in or near regulatory QTL. These incompatibilities often resulted in alteration in the protein-coding regions of the novel transcripts in the form of frameshifts and truncations. By associating the splice variation in these genes with size and growth rate measurements, we found that the cumulative expression of all aberrant transcripts was correlated with a significant reduction in growth rate. Our results lead us to propose a model where divergent splicing regulatory loci could act as incompatibility loci that contribute to the evolution of reproductive isolation.<\/p>\n\n\n\n