The goal of mapping expression quantitative trait loci (eQTLs) is to identify genomic regions regulating gene expression traits, which can be gathered through microarrays, RNA-Seq, or related methods. Because thousands of expression traits are analyzed simultaneously, eQTL analysis can help elucidate regulatory networks and provide valuable insights into the molecular mechanisms underlying complex traits. Numerous eQTL studies have been conducted to delineate regulatory networks in various organisms, and they have led to many significant findings. In this chapter, we provide a step-by-step protocol for genome-wide eQTL mapping and downstream analysis.