In various embodiments, the present disclosure provides an automated seed sampler system that includes a milling station (400) for removing at least a portion of seed coat material from a seed and a sampling station (500) for extracting a sample of seed material from the seed where the seed coat has been removed. A seed transport subsystem (600) conveys the seed between the milling station (400) and the sampling station (500) and a seed deposit subsystem (1000) conveys the seed from the seed transport subsystem (600) to a selected well in a seed tray (18) after the seed has been sampled.
