The study of biological processes has been aided greatly by the development of procedures to identify the large numbers of associated genes. However, the ability to study the identified genes experimentally is often impeded by the absence of technologies to perform such functional analyses. Here, a nonaxenic plant transformation system has been developed in Gossypium hirsutum (cotton) for the study of genes associated with root functions and root-organism interactions. The plant transformation system is compatible with modern high throughput plant transformation goals and the processing of large numbers of genes intended for the study of root function in G. hirsutum.