The present invention provides for novel methods to facilitate germplasm improvement activities through the use of high throughput, nondestructive sampling of seeds. In one embodiment, a high-throughput, non-destructive method for analyzing individual seeds in a population of seeds comprises removing a sample from a plurality of seeds in the population while preserving the germination viability of the seed and analyzing the sample for the presence or absence of one or more characteristics of at least one genetic or chemical trait.