This invention relates generally tothe detection of genetic differences among soy-beans.More particularly, the invention relates tosoybean quantitative trait loci (QTL) for toleranceto protoporphyrinogen oxidase inhibitors, to soy-beanplants possessing these QTLs, which map toa novel chromosomal region, and to genetic markersthat are indicative of phenotypes associatedwith protoporphyrinogen oxidase inhibitor tolerance.Methods and compositions for use of thesemarkers in genotyping of soybean and selectionare also disclosed.