The invention relates to a method for analysing maternal DNA of a seed, comprising the steps of contacting a seed with a fluid to dislodge DNA from the seed coat surface, and analysing the DNA. Suitably, the fluid is comprised in a container and the container is part of an automated system for high-throughput analysis of maternal DNA in large plant populations. The invention further provides a method for examining the maternal genome of the seed through analyzing maternal DNA, wherein the DNA is obtained by the method.
