The disclosure relates to improving plant breeding methods by controlling for microbial diversity present in the plant breeding process. The resent disclosure addresses a great need in the art, by providing for improved plant breeding methods that do not suffer from many of the drawbacks inherent with current methodologies. For instance, the methods of the present disclosure are able to capture and harness a previously untapped resource, the microbiome, and utilize such to improve traditional plant breeding methods. That is, the methods taught herein are able to control for, and beneficially harness, the microbial communities present in the plant breeding process
