Fig. 1 Location and the admixture analysis of the 223 ponderosa pine genotypes. Left: Original geographic distribution of the 223 ponderosa pine genotypes. Right: Proportion of each individual’s genome allocated to “population 1” (green) and “population 2” (orange) by admixture analysis when K=2, illustrating lack of geographical isolation. Trees were subsequently treated as part of a single population.
Fig. 2 Venn diagram comparing overlap in environmentally associated SNPs. The number of overlapping SNPs that are associated with four climatic variables between April 1stsnowpack (PCK4), monthly winter precipitation (PPTW), climatic water deficit (CWD), and minimum winter temperature (TMIN).
Fig. 3 Venn diagram comparing overlap in phenotypically associated SNPs. Left: Overlap in SNPs significantly associated with control root length (RL), root-shoot ratio (R2S), and abaxial stomatal rows (NR_AB). SNPs associated with control height growth (15), adaxial stomatal density (12), and shoot weight (9) did not overlap with other categories. Right: Overlap in SNPs significantly associated with drought responsiveness of shoot weight (\(\Delta\)SW); root length (\(\Delta\)RL); and the number of stomatal rows on abaxial side\(\ (\Delta NR\_AB)\). SNPs associated with drought responsiveness of height growth (150), adaxial stomatal density (57), and R2S (6) did not overlap with any other categories.
Fig. 4 Five types of annotated SNP functions associated with different climatic variables. The number of non-synonymous variants and other variants that are associated with the five climatic variables: Climatic water deficit (CWD); Minimum winter temperature (TMIN); Maximum summer temperature (TMAX); April 1st snowpack (PCK4), and Monthly winter precipitation (PPTW). Missense (non-synonymous) SNPs are shown in grey, and other types of SNP are in orange.
Fig. 5 Five types of annotated SNP functions associated with different traits in control conditions . The number of non-synonymous variants and other variants that are associated with four traits in control conditions: root length (RL), number of stomatal rows on abaxial surface (NR_AB), stomatal density on adaxial surface (SD_AD), and root-to-shoot ratio (R2S). No SNPs in these categories were associated with height growth or shoot weight. Missense (non-synonymous) SNPs are shown in grey, and other types of SNP are in orange.
Fig. 6 Five types of annotated SNP functions associated with drought responsiveness of different traits. The number of non-synonymous variants and other variants that are associated with drought responsiveness of five traits: changes in height growth (GR), root length (RL), shoot weight (SW), number of stomatal rows on abaxial surface (NR_AB), and stomatal density on adaxial surface (SD_AD). No SNPs in these categories were associated with root-to-shoot ratio (R2S). Missense (non-synonymous) SNPs are shown in grey, and other types of SNP are in orange.