The wild tomato Lycopersicon pennellii is resistant to numerous important pests of cultivated tomato, L. esculentum, including armyworm, fruitworm, aphids, leafminers, and whitefly. The pest resistance of L. pennellii is mediated by the presence of acylsugars, which constitute 90% of L. pennelliitype IV trichome exudate. Transfer of the ability to accumulate acylsugars could result in pest-resistant tomato cultivars, and thus, a reduction in the dependence on synthetic chemicals for insect control for this crop. Initial tomato lines bred for acylsugar production possessed the desired insect resistance, but were of poor horticultural quality due to linkage drag. These tomato lines possessed seven or eight L. pennellii introgressions, some of which were quite large. As a result, about 25% to 30% of the genomes of these acylsugar lines were comprised of L. pennellii DNA. A set of 20 molecular markers was created, providing markers throughout each introgression. The acylsugar breeding program then combined use of a biochemical assay for acylsugars and genomic analyses using these molecular markers to determine which of the introgressions were involved in the linkage drag, and to select plants that either eliminated or shortened those introgressions. Introgressions on chromosomes 2, 3, 5, and 10 were found to be associated with negative characteristics, such as delayed germination, reduced fruit set or size, delayed maturity, or reduced seed set. New acylsugar lines that eliminate or reduce some of these introgressions were created. The new lines show marked improvement in some of the affected traits, while also producing acylsugars. Hybrids created using these lines show marked improvement in horticultural type.