A method is provided for removing tissue samples from seeds. The method generally includes orienting the seeds in a desired orientation and removing tissue samples from the oriented seeds. The method may also include orienting the seeds in the desired orientation using an actuator, where the actuator is configured to position the seed in a desired orientation. In addition, the method may include orienting the seeds together in a seed transport and removing tissue samples from the oriented seeds while the oriented seeds are in the seed transport. Further, various operations of the method may be automated as desired, for example, to permit greater sampling throughput than was previously practical.