Much of Tanksley's work focused on identifying alleles from wild relatives of crops that could be useful in improving cultivated varieties, for example fruit size and shape in tomato, using the technology Marker-assisted selection (MAS). He led work developing the advanced backcross Quantitative Trait Loci (QTL) method, facilitating the introgression of new alleles into cultivated breeding lines. His team also spearheaded using genetic markers in comparative mapping among Solanaceae species and others.