Targeted-Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome

Whitebark pine (Pinus albicaulis) covers an expansive range in western North America, and is considered a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and is suffering significant mortality range-wide, prompting the tree to be listed as “globally vulnerable” by the IUCN, and “endangered” by the Canadian government.  Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based capture to enrich targeted genomic regions from the 30⁺ GB genome of whitebark, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 sites), and we were able to identify 12,390 segregating sites from 47 trees. Variation at SNP sites reveals strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that targeted capture produces high quality, codominant genotypes from the large genome of whitebark, and the resulting data can be readily integrated into management and gene conservation activities.