 The text was simplified as follows, abstract background cryptic genetic variation, CGV, is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode kinohugditis elegans. We analyzed regulatory variation in gene expression and MACDQTL across the course of a heat stress and recovery response in a recombinant inbred population. Results we measured gene expression over three temperature treatments, i.e. control, 2. heat stress, and 3. recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3,305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat stress. This article was authored by Basten L. Snoke, Mark G. Sturkin, Role P. J. Beavers, and others. We are article.tv, links in the description below.