Fig 1.
Locations of seed families and geographic distribution of genetic subgroups.
A total of 124 seed families were samples in 16 seed (sub) zones. Each pie chart represents the proportion of genetic subgroups (GG-1 to GG-9) as identified by STRUCTURE in a given area.
Fig 2.
Classification of DNA variation in the whitebark pine transcriptome.
Single nucleotide polymorphism (SNP), multiple nucleotide variation (MNV), and small insertions or deletions (InDel) were detected using CLC Genomics Workbench (v5.5). Synonymous and nonsynonymous SNPs (s-SNP and ns-SNP) were determined in the coding DNA sequences (CDS).
Fig 3.
Principal coordinate analysis (PCoA) of whitebark pine populations using GenAlEx version 6.5.
Seed zone (subzone) designations were listed in S1 Table. Three regions are shown by colors, Green: British Columbia (BC), Canada; red: Washington State (WA); blue, Oregon state (OR), USA.
Fig 4.
Phylogenetic relationships among whitebark pine populations.
Nei’s standard genetic distances with sample size correction (Dst) (Nei 1972) were calculated using genotypic data of 71 SNP loci. A consensus dendrogram was constructed using the unweighted pair-group method with arithmetic mean (UPGMA). Bootstrap values are indicated on the nodes as percentages as tested with 1000 bootstrap replicates.
Fig 5.
Analysis of Molecular Variance (AMOVA) of whitebark pine samples collected in western North America for a breeding program.
(A) AMOVA based on seed families. (B) AMOVA based on seed (sub) zones.
Fig 6.
Bayesian clustering analysis for estimation of population structure using program STRUCTURE.
ΔK plots by Evanno’s method. 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. Genotypic data were collected for 71 ns-SNP loci across all genotyped individuals. The highest peak shows the best K = 9.
Fig 7.
Population structure as shown by bar plot of the estimated membership coefficient (Q) of genotyped samples with SNPs matrix.
All genotyped samples were clustered into nine subpopulations (genetic subgroups GG-1 to GG-9). Numbers of individuals assigned to each genetic group are shown in round brackets. Each vertical bar represents one sample, and a subpopulation (genetic subgroup) is shown in one main color. In the vertical bar, the length of each K colored segment corresponds to the proportion of alleles contributed by each of the K subpopulations.
Fig 8.
Association of whitebark pine genetic subgroups with relative levels of disease severity post inoculation by Cronartium ribicola.
(a) Mean values of relative levels of disease severity were shown for seedlings with nine genetic subgroups (GG1 to GG9). Standard error (SE) was calculated based on the entire subpopulation of each genetic subgroup. Statistical difference is significant (T-test and One-way ANOVA test, * P < 0.05, ** P <0.01) between subgroups labelled with different letters.