A system and method for preparing a sample of seeds or representative seed portions are provided. In various embodiments, the system and method include a force applying member and a seed container that includes at least one compartment containing a seed. The force applying member is configured to apply a force to the seed so as to break the seed into two or more seed particles, which in some embodiments may be collected in a seed particle collector. The present invention improves on the prior art by greatly reducing (and in some embodiments eliminating) the manual processes typically involved in generating tissue samples from seeds and preparing the tissue for genetic analysis. Additionally, the present invention is scaleable, and can be configured to generate samples from many seeds in a short period of time. The present invention also minimizes the risk of contamination and cross-contamination of the seed particles.