Genomic exploration of Thuja plicata indicates no loss of diversity from adults to offspring in UK Woodlands

Abstract Thuja plicata is a conifer tree that is valued for its cultural, ecological and wood quality features in its natural range in western North America and is used in Europe as an exotic timber species. It is increasingly used in mixed species forests in the UK that are managed using natural regeneration, raising questions about genetic diversity of both the adult trees and offspring of the species in these stands. We studied population structure and genetic diversity in four UK woodlands of both adults and naturally regenerated offspring of T. plicata . We discovered 194,154 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 655 SNPs across 598 genome sequence scaffolds for analysis. The majority of these scaffolds included only one SNP, suggesting that; the selected SNPs were widely distributed within the genome. We found many monomorphic sites, most of which were restricted to adults in a single woodland, indicative of a genetic differentiation among woodlands. We found three ancestral populations (K = 3) and low levels of admixture across the four sites, indicating that the starting materials were largely from single populations. Estimates of genetic diversity using heterozygosity (H o ) and nucleotide diversity (π) were low (overall H o = 0.174, π = 0.00226) across all sites but slightly higher in juveniles at two sites. Our genotyping methods and results on standing genetic diversity in this important conifer provide insight into the ability of planted woodlands in the UK to face environmental shifts and disease threats.