1. An automated seed sampler system, comprising: a milling station for removing at least a portion of seed coat material from a seed; a sampling station for extracting a sample of seed material from the seed where the seed coat has been removed; a seed transport subsystem for conveying the seed between the milling station and the sampling station; and a seed deposit subsystem for conveying the seed from the seed transport subsystem to a selected well in a seed tray after the seed has been sampled.