Embryogenesis is a process in biology when the embryo forms and takes shape. While being a hallmark event, knowledge about this tightly orchestrated process is scarce. One of the reasons is limitations of studying this event in mammals and humans (obviously we cannot study it easily in humans for ethical reasons). Cannavò et al. took a model-organism based approach and studied the genetic regulation of embryogenesis using inbred isolates of Drosophila. The authors collected samples as different time-points during embryogenesis, and used a modified RNA-seq protocol to capture 3′ end of transcripts, providing quantitative measurements of poly(A)-site usage and gene expression. The former is useful to map out usage of alternative 3′ untranslated regions (this information is not available in regular RNA-seq). The authors then used a mixed linear model to generate quantitative trait loci (mapping out influence of genetic variants on molecular traits measured by RNA-seq). The authors generate so-called utrQTLs – reflecting genetic variants impacting 3′ RNA processing. A total of 17% of expressed genes were affected by a QTL, suggesting complex allelic interactions during embryogenesis.