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I am assuming you want to monitor these traits in controlled conditions because in wild type conditions it will be real challenge to monitor in details unless you have easily accessible way (like leave surface area and related visual traits). Remember these techniques will change according to your plant/seed and your study interest. Lot of things change ...


Most NGS approaches should enable you to sequence all those plasmids at very low cost-per-base values (Please see here for more on prices). The challenge in sequencing them all, if there are sequences common to all your plasmids, will be to get adapters for each sample/plasmid so that reads can be mapped back to the correct plasmids.

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