crops such as corn, sorghum and soybean. While FAW larvae are considered polyphagous, differences in diet preference have been described between two genetic variants: the Corn strain (sf-C) and the Rice strain (sf-R). These two strains are sometimes considered as distinct species, raising the hypothesis that host plant specialization might have driven their divergence. Ecological speciation takes place when adaptations to different ecological niches lead to the reproductive isolation of two populations. Under this hypothesis, we expect that the transcriptional response to the host plants should affect differently the fitness of the two FAW strains. We also expect that these genes should also be linked to a reproductive isolation mechanism between the strains. In this study, we performed controlled reciprocal transplant (RT) experiments to address the impact of plant diet on several traits linked to the fitness of the sf-C and sf-R strains. The phenotypical data suggest that sf-C is specialized to corn. We then used RNA-Seq to analyze the gene expression of FAW larvae from RT experiments. We show that each strain has a different response to the same plant diets. However, we also found constitutive transcriptional differences between strains in laboratory and in natural populations. In particular, we show that mitochondrial transcription is the main difference between strains. A difference in mitochondrial function may be the basis for a shift in host plant and could be involved in hybrid incompatibility, raising the hypothesis that mitochondrial genome is the main target of selection between the two strains.. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. (Goergen et al. 2016;Jeger et al. 2017).The FAW is a polyphagous species, being documented on over 100 plants from 27 different families (Pogue 2002). However, using allozymes electrophoresis monitoring, a significant genetic heterogeneity has been observed in FAW . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/263186 doi: bioRxiv preprint first posted online Mar. 5, 2018; 4 populations that was associated with feeding preferences (Pashley et al. 1985;Pashley 1986). One genetic haplotype was mostly found on corn (Zea mais), sorghum (Sorghum spp.) and cotton (Gossypium spp.) and was named the corn strain (sf-C). Another haplotype was found associated to individuals collected on smaller grasses such as turf, pasture (Cynodon dactylon) grasses and rice (Oryza spp.), and has been named the rice strain (sf-R) (Pashley 1988). Subsequent studies have confirmed these genetic differences on markers such as the mitochondrial gene Pashley and Martin 1987;Pashley, Hammond, and Hardy 1992). In order to detect post-zygotic...