Variables affecting DNA preservation in archival plant specimens

Tue, 2015-04-28 15:52 -- aflemming
TitleVariables affecting DNA preservation in archival plant specimens
Publication TypeJournal Article
Year of Publication2014
AuthorsNeubig, Kurt M., Whitten Mark W., Abbott Richard J., Elliot Savannah, Soltis Douglas E., and Soltis Pamela S.
JournalDNA Banking for the 21st Century
Start Page81
Date Published2014
ISBN Number 0-9808415-9-8
AbstractAlthough the use of plant DNA in scientific research is now decades old now. we still know very little about the best methods of DNA preservation. A few studies have addressed aspects of DNA quality and preservation . but a broad sense of the quality of DNA in herbarium specimens and tissues specifically preserved for DNA usage is still lacking. This article reviews the basic concepts ofDNA preservation, factors affecting DNA in herbarium specimens. optimal methods for DNA extraction. and storage. To address lingering questions about the nature ofDNA quality in archival plant specimens. we also evaluated - 2000 samples from herbarium specimens. as well as silica-dried and frozen tissuesspecifically preserved for DNA usage. For herbarium specimens. we used materials spanning much of angiosperm phylogenetic diversity to ascertain general trends of DNA degradation over time and to assesswhether different clades had different rates of "expiration." Our results indicate different rates ofDNA degradation , but for mostsamples. no matter the taxonomic group . we were unlikely to recover high-quality DNA after 30-40 years. Nonetheless, given rapid technological advances and changes in DNA sequencing methods. even herbarium specimens with highly degraded DNA may still be of use in molecular analyses. Additional herbarium specimens were sampled for two different collection sets with drastically different curation histories bur of approximately the same age. This analysis showed a vety marked difference in DNA quality between the two sets: the well-curared specimens had excellent-quality DNA while the poorly curated samples had low-quality DNA. For frozen tissues, virtually all samples had excellent quality. whether storage wasat -20· or -BO·C and whether tissue was pulverized or intact. For silica-dried tissues, the results were much more heterogeneous, depending on the storage vessel. Samples stored in vessels with poor seals yielded lower-quality DNA. To address the long-term viability of frozen DNA extracts, we compared a set of 7-I2-year-old DNA extracts with new extracts of the same original silica-dried tissues and with fresh, greenhouse-collected tissues of the same original material, these comparisons indicared less degradation in the extracts than in rhe silica-preserved samples, although the differences were subtle. We also found that IS-year-old photo-bleached, silica-dried samples Still had small amounts of high-molecular-weighr DNA. The long-term preservation of DNA in archival samples remains problematic. bur we can besr preserve DNA by limiting the factors that degrade it. Although the botanical community has been preserving tissues and DNA extracts for a limited umespan, we can infer some basic conclusions from this and oth er studies . Recommended best practices are to freeze tissues and extracts at as Iow a rernperarure as possible (e.g., -BO·C). bur if that is not possible or practical. room temperature storage of rlssues with silica in tightly sealed containers is a viable alternative , at least for the short term.