GT-seq - Genetic differentiation in Calamagrostis species

There is growing demand for data driven frameworks to guide robust plant restoration strategies in response to anthropogenic disturbances. Several seed sourcing strategies, that is provenancing strategies, have been proposed which balance the use of locally adapted genotypes against mixed genotypes to reduce mutation load or to assist migration in anticipation of future climate scenarios. However, taxonomic uncertainty and lack of data characterizing genetic differentiation and gene flow have hindered provenancing strategies for many ecologically important non model plant species, especially those in remote but vulnerable regions such as the boreal forests of northern Canada. To guide provenancing strategies following anthropogenic disturbance in the Northwest Territories of Canada, we characterize species specific markers, population structure, and hybridization among three Calamagrostis species. Double digest RAD sequencing, abbreviated as ddRAD, resulted in two thousand nine hundred fifty one polymorphic loci across twenty seven individuals, which we used to design loci for genotyping in thousands by sequencing, abbreviated as GT seq, a cost efficient target loci approach that produced two hundred fifty six polymorphic loci across ninety three individuals from wild Calamagrostis canadensis, Calamagrostis stricta subspecies inexpansa, and Calamagrostis purpurascens populations. To help define the scale of local populations for seed sourcing, we characterized geographic variation and population structure among fifty seven wild collection sites. We also assessed genetic relationships of wild Calamagrostis canadensis to sixty nine individuals across eight commercially maintained populations used in restoration projects. We found that GT seq yields similar patterns of genetic differentiation as common neutral molecular marker approaches such as ddRAD sequencing. Specifically, we resolved morphologically misidentified individuals, identified genetic hybrids, and characterized the scale of genetic isolation by distance. Finally, we determined that three cultivar seed sources were genetically similar to southern wild populations, whereas five cultivars aligned with northern wild populations of Calamagrostis canadensis in the Northwest Territories of Canada. Overall, our results highlight the benefits of cost effective methods for genome wide multilocus genotyping to inform provenancing best practices and to support more effective and sustainable restoration efforts.