Abstract: Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTL). It is a great challenge for scientists and breeders to identify key genes or superior alleles underlying these important QTL in crops. This review summarizes recent progress in the study of QTL mapping and cloning, including QTL primary mapping, QTL fine mapping and positional cloning, the development of QTL-NILs and SSSLs, and LD-based association analysis. A combination of linkage mapping and association analysis, supported by the latest developments in genomics platforms, should be an efficient strategy for QTL mechanism research as well as QTL adoption in plant breeding.