Genome-wide SNP diversity in natural and cultivated populations informs restoration ecology with three Calamagrostis species from the Northwest Territories of Canada

Abstract

There is growing demand for data-driven frameworks to guide robust plant restoration strategies in response to anthropogenic disturbances. Several seed-sourcing (i.e., provenancing) strategies have been proposed, which balance the use of locally adapted genotypes against mixed genotypes to reduce mutation load or assistant migration to anticipate 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 like the boreal forests of northern Canada. To guide provenancing strategies following anthropogenic disturbance in Canadas Northwest Territories, we characterize species-specific markers, population structure, and hybridization among three Calamagrostis species. Double digest RAD sequencing (ddRAD) resulted in 2,951 polymorphic loci across 27 individuals, which we used to design loci for genotyping in thousands by sequencing (GT-seq), a cost-efficient target loci approach resulting in 256 polymorphic loci across 93 individuals from wild C. canadensis, C. stricta ssp. inexpansa and C. purpurascens populations. To help define the scale of local populations for seed sourcing, we characterized geographic variation and population structure among 57 wild collection sites. We also assessed genetic relationships of wild C. canadensis to 69 individuals across eight commercially maintained populations used in restoration projects. We found that GT-seq yields similar genetic differentiation patterns as common neutral molecular marker approaches like ddRAD-seq. Specifically, we resolve morphologically misidentified individuals, identify genetic hybrids, and characterize 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 C. canadensis in the Northwest Territories of Canada. Overall, our results highlight the benefits of cost-effective methods for genome-wide multi-locus genotyping to inform provenancing best-practices and support more effective and sustainable restoration efforts.