Novel methods are provided to facilitate germplasm improvement activities through the use of high throughput, nondestructive sampling of seeds. A method for introgressive hybridization, for example, generally includes removing tissue samples from individual seeds using an automated seed sampler without affecting germination viability of the seeds, and analyzing nucleic acids extracted from the tissue samples for at least one genetic marker. The method then further includes selecting the sampled seeds that possess the at least one genetic marker, cultivating fertile plants from the selected seeds, and crossing the fertile plants with other plants.