Graph of delta K values (y-axe) against assumed sub-populations (x-axe) showing the ideal number of groups present in a set of whitebark pine seed families collected for a breeding program. (B) AMOVA based on seed (sub) zones.īayesian clustering analysis for estimation of population structure using program STRUCTURE. Bootstrap values are indicated on the nodes as percentages as tested with 1000 bootstrap replicates.Īnalysis of Molecular Variance (AMOVA) of whitebark pine samples collected in western North America for a breeding program. A consensus dendrogram was constructed using the unweighted pair-group method with arithmetic mean (UPGMA). Nei’s standard genetic distances with sample size correction (Dst) (Nei 1972) were calculated using genotypic data of 71 SNP loci. Phylogenetic relationships among whitebark pine populations. Three regions are shown by colors, Green: British Columbia (BC), Canada red: Washington State (WA) blue, Oregon state (OR), USA. Seed zone (subzone) designations were listed in S1 Table. Principal coordinate analysis (PCoA) of whitebark pine populations using GenAlEx version 6.5. Synonymous and nonsynonymous SNPs (s-SNP and ns-SNP) were determined in the coding DNA sequences (CDS).

Single nucleotide polymorphism (SNP), multiple nucleotide variation (MNV), and small insertions or deletions (InDel) were detected using CLC Genomics Workbench (v5.5). Each pie chart represents the proportion of genetic subgroups (GG-1 to GG-9) as identified by STRUCTURE in a given area.Ĭlassification of DNA variation in the whitebark pine transcriptome. Locations of seed families and geographic distribution of genetic subgroups.Ī total of 124 seed families were samples in 16 seed (sub) zones.

Clc genomics workbench 9