Traceability of provenance-collected lodgepole pine in a reforestation chain of custody case study

Millions of lodgepole pine seedlings are planted each year to replace losses due to harvest or large-scale natural disturbances such as fires and forest pests. In Canada, replacement seeds and seedlings used for reforestation are often regulated by explicit policies. For example, in the province of Alberta, seedlings must be grown from seeds collected within a strictly defined zone that includes the harvested area where the seedlings will be planted. Thus, traceability along the entire reforestation chain of custody, from seed collection to seedling outplanting, is vital to ensure policy compliance. Here, we report a case study in which we used genomic tools to determine if seedlings were sown from a contaminated seed source. The 165,000 seedlings under scrutiny were scheduled for deployment the same year in which the seeds were sown, necessitating fast processing to make decisions on deployment. The scenario was made more complex by the fact that most of the potentially contaminated seed sources represented wild-collected genetic material in close geographic proximity to each other, rather than pedigree genetic material. With genotyping data obtained from a high-density single nucleotide polymorphism array analyzed with clustering analyses, kinship estimations, and genetic assignment tests, we were able to determine the probable seed source of this suspect group of seedlings and make data-guided recommendations on whether these seedlings could be confidently deployed onto the landscape without violating policy guidelines. This case study demonstrates the unique utility of molecular markers to confidently assign seedlings to a non-pedigree parent seed source originating within a limited geographic range, thereby ensuring traceability within a reforestation pipeline.