New genetic markers for 100% arabica coffee demonstrate high discriminatory potential for InDel-HRM-based coffee authentication

Food authenticity is crucial in today's society, given the heightened consumer awareness and attention to the products they consume. Reliable and efficient techniques are needed to quickly detect potential food adulterations that can negatively impact product quality and economic value. Coffee, a globally traded agricultural product, holds immense economic importance, with an estimated value of USD 83 billion. It is widely consumed and recognized as a functional food that provides minerals (K, Mg, Mn, Cr), niacin, and antioxidants. However, the preferred coffee species, Coffea arabica, known for its superior drink quality, is often adulterated with Coffea canephora (Robusta and Conilon) beans, even in 100% Arabica coffee. To distinguish between these two coffee species, a comprehensive study was conducted using a robust approach to identify differences in Single-Ortholog Copy (SOC) based on InDel regions in these gene pairs. These differences were validated using a meticulous methodology that considered variations in amplicon size: electrophoretic profile, and high-resolution melting (HRM). The innovative combination of InDels and HRM resulted in highly distinctive HRM profiles, outperforming SNP-based methods previously used. The targeted InDel approach utilized in this study facilitated precise quantification of Coffea species beans with a detection sensitivity of 0.5%. The study's findings establish the reliability and accuracy in distinguishing between the two coffee species, showcasing the valuable application of InDels for quality control and ensuring the authenticity of coffee beans. This pioneering research contributes to the advancement of authenticity verification methods for both imported and exported coffee beans, as well as in future studies that require significant genetic differences between these species, such as C. arabica and C. canephora.