An effective method for analyzing the genetic makeup of complex traits in a variety of taxa, including people, plants, and animals, is quantitative trait loci (QTL) analysis. QTL studies offer important insights into the genetic basis of variables like disease susceptibility, agronomic attributes, and behavioral traits by finding genomic areas linked to phenotypic variance. The goal of this article is to give a thorough introduction to QTL analysis, covering its foundational ideas, methods, and various applications. The theoretical underpinnings of QTL mapping are covered, with a focus on the statistical methods used to identify and map the genetic areas that affect quantitative traits. In addition, we discuss how improvements in experimental designs?such as association and linkage mapping?allow for the highly accurate and precise identification of QTL. We also emphasize how QTL analysis is multidisciplinary and encompasses genetics, genomics, bioinformatics, and statistical genetics. In order to clarify the molecular mechanisms underlying complex traits, we address the integration of QTL mapping with functional genomics techniques including genome-wide association studies (GWAS) and gene expression profiling.