This invention relates generally to the detection of genetic differences among soybeans. More particularly, soybean quantitative trait loci (QTL) associated with herbicide tolerance, including tolerance to one or more of an HPPD-inhibitor herbicide, such as mesotrione and isoxazole herbicides, and/or a PPO inhibitor herbicide； soybean plants possessing these QTLs； and genetic markers that are indicative of phenotypes associated with such herbicide tolerance are provided. Methods and compositions for use of these markers in genotyping of soybean and selection are also disclosed, as are methods and compositions for use of herbicides for weed control. Also disclosed are isolated polynucleotides and polypeptides relating to such tolerance or sensitivity and methods of introgressing such tolerance into a plant by breeding or transgenically, or by a combination thereof. Plant cells, plants, and seeds produced are also provided.
