An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

Abstract

Whitebark pine is difficult to distinguish from limber pine when seed cones are not present. This is often the case because of young stand age, growth at environmental extremes, or harvesting by vertebrate species. Developing an economical genetic identification tool that distinguishes non-cone-bearing limber from whitebark pine, therefore, could aid many kinds of research on these species. Phylogenetic studies involving limber and whitebark pine suggest that chloroplast DNA sequences differ between these species. We therefore wanted to identify chloroplast loci that could differentiate limber from whitebark pine trees by taking an economical approach involving restriction-site analysis. We generated chloroplast DNA barcode sequences sampled from limber and whitebark pine trees that we identified using attached seed cones. We searched for nucleotide differences associated with restriction endonuclease recognition sites. Our analyses revealed that matK and the psbA-trnH spacer each readily amplified and harbored multiple DNA-sequence differences between limber and whitebark pine. The matK coding sequence of whitebark pine has a BsmAI restriction site not found in limber pine. The psbA-trnH spacer of limber pine has two PsiI restriction sites, neither of which is found in whitebark pine. DNA-sequence and restriction-site analysis of the psbA-trnH spacer from 111 trees showed complete congruence between visually and genetically identified limber (n = 68) and whitebark (n = 43) pine trees. We conclude that restriction site analysis of the chloroplast psbA-trnH spacer and matK involves both minimal technical expertize and research funds. These findings should be of value to foresters interested in species identification and distribution modeling, as well as the analysis of fossil pine pollen, given that gymnosperms transmit chloroplast DNA paternally.

Growth, drought response, and climate‐associated genomic structure in whitebark pine in the Sierra Nevada of California

“…We minimized the potential for species misidentification by sampling within areas of known whitebark pine presence, focused on large trees that have field identification characteristics such as male and female cones, and used extremely experienced field crews. To further confirm species identification, we tested a subset of samples using a molecular assay that distinguishes whitebark from limber pine based on differences in chloroplast genes (see Alongi et al, 2019 for methods). All samples were confirmed as whitebark pine.…”

Rheological and mechanical study of micro-nano sized biocarbon-PLA biodegradable biocomposites

“…This fungus was unintentionally brought from Europe to North America, where it has devastated native white pine trees throughout the continent, especially the closely related whitebark pine. Siberian pine is statistically significant for hybridization and genetic modification studies to create rust resistance in these species (Kuznetsova 2008;Alongi et al 2019).…”