The present invention provides for novel methods to facilitate germplasm improvement activities through the use of high throughput, nondestructive sampling of seeds. A method of evaluating seeds for a desired trait, for example, for facilitating germplasm improvement activities, etc., generally includes removing tissue samples from individual seeds using an automated seed sampler without affecting germination viability of the seeds, analyzing the tissue samples for one or more characteristics indicative of a desired trait, and selecting the sampled seeds that include the desired trait.