The genetic improvement of Upland cotton (Gossypium hirsutum L.) has been hindered by a narrow gene pool. Genetic diversity can be acquired through different breeding methods such as chemical mutation using ethyl methanesulfonate (EMS) and introgression of exotic genes. The primary objective of this study was to investigate potential linkage drag associated with traits that have been derived from the two above breeding approaches. We evaluated 10 EMS-derived mutant populations originally selected for fiber quality traits to determine if the mutation process caused any negative effects on agronomic characteristics. Data suggests that agronomic traits did not experience negative effects. Also, we evaluated the agronomic and fiber quality traits of root-knot nematode-resistant cotton germplasm derived from introgression. The results suggest that agronomic and fiber quality traits were not impacted by the resistant QTLs. However, lint percentage may be negatively affected, which can be overcome by breeding efforts.