Bioinformatics is an interdisciplinary field that has been playing key roles in understanding biology and medicine. Currently, bioinformatics education faces several challenges, including incomplete understanding of the overall knowledge system of the discipline, lack of in-depth understanding of theory, limited hands-on practice opportunities. These issues make it difficult for students to integrate theoretical knowledge with practical applications, thereby weakening their innovative capabilities and ability to solve real-world bioinformatics problems. To address these challenges, we propose an approach that integrates history, theory, and practice, and applies it to the reform of bioinformatics teaching. Taking the analysis of expression quantitative trait loci (eQTL) as an example, we show how to incorporate historical context, theoretical knowledge, and actionable projects into course teaching. This reform aims to promote the interest, practical skills, and innovative abilities of students, providing a reference for training high-quality bioinformatics talent.