The present invention provides for novel methods to facilitate germplasm improvement activities through the use of high throughput, nondestructive sampling of seeds. A method for analyzing a population of haploid seeds generally includes providing a population of seeds comprising haploid seeds, removing tissue samples from a plurality of the seeds in the population using an automated seed sampler system while preserving the germination viability of the sampled seeds, and analyzing the tissue samples for the presence or absence of one or more characteristics indicative of at least one genetic or chemical trait.