The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes methods for assaying a location to determine the amount of pest infestation, or assaying a plant for its ability to resist infection, and using this information to make agronomic treatment and/or breeding decisions. The invention also provides methods for breeding cotton plants containing one or more quantitative trait loci that are associated with resistance to reniform nematode infection. The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring reniform resistance as a source of reniform resistant alleles for introgression into elite germplasm in a breeding program, thus producing novel elite germplasm comprising one or more reniform resistance loci.