Are Transcriptional Responses to Inbreeding a Functional Response to Alleviate Inbreeding Depression?

Previous studies addressing the relationship between gene regulation and inbreeding depression did not allow for discerning the changes that alleviate the depression from those that generate it. We directly addressed this question by analyzing changes in gene expression, using Affymetrix 2.0 arrays in Drosophila melanogaster inbred sublines differing in their magnitudes of inbreeding depression relative to the expression in an outbred control. The total number of arrays analyzed was 27, with 9,133 probe sets showing a significant signal of expression. We found that for those genes differentially expressed between inbred and outbred sublines, most of them showed a pattern of expression consistent with a protective role against inbreeding effects. The observed increase in depression was presumably related to an inability of the genome to do the appropriate expression adjustments. Expression changes detected in our study showed a clear specificity of RNA-splicing and energy derivation functions. Thus, it appears that most of the observed changes in gene expression associated with inbreeding may occur predominantly to alleviate inbreeding depression, i.e., as a protection against the effects of inbreeding.