DNA preservation and utility of a historic seed collection

Abstract

Historic collections of biological material are important genetic resources for taxonomic, evolutionary and historical research. In this paper we describe a seed collection dating from 1862 to 1918 maintained at the Swedish Museum of Cultural History. The collection contains over 3000 well-documented seed samples of various agricultural crops, mostly cereals. A subset of 100 samples divided over ten species frequently represented in the collection and a range of ages were tested for germinability and DNA preservation. None of these accessions were found to contain viable seeds. DNA extracted from the seeds was degraded, but the amount of degradation varied between species. DNA quality was evaluated by yield, fragment size and size of amplification product. Quality was highest for DNA extracted from Pisum sativum and Vicia sativa. DNA extracted from Brassica napus, Beta vulgaris and Trifolium pratense was more fragmented, and DNA extracted from Triticum aestivum, Secale sereale, Hordeum vulgare, Avena sativa and Phleum pratense was most degraded. Polymerase chain reaction (PCR) amplification of ribosomal DNA fragments of up to 700 bp was permitted for most samples in all species. To test whether single-copy nuclear genes could be amplified from the extracted DNA, microsatellite markers were used on the Pisum sativum and Hordeum vulgare samples. Polymorphisms of microsatellite markers were detected between samples for both species. The results show that the 19th-century seed collection can be utilized to infer genetic relationships among obsolete cultivars as well as for other types of genetic research based on sequence or marker analysis.

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

“…Of these the majority, 31 accessions, were taken from the nineteenth century historical seed collections; Tromsø University Museum in Norway (TR, three accessions), Mustiala Agricultural College in Finland (MU, six accessions) and the Swedish Museum of Cultural History in Sweden (NM, 21 accessions) (Leino et al, 2009;Leino, 2010). The seeds, which are no longer viable, were collected at harvest on farm in 1869 (TR), 1890s (MU) and 1896 (NM), respectively, except for NM264 that was collected in 1882.…”

“…DNA from barley seeds in the historical collections is degraded to fragments of typically 100-200 bp and yield 200 ng mg − 1 seed, compared with extant seeds where DNA yield is typically four times higher and DNA length is above 10 000 bp (Leino et al, 2009). DNA concentrations in the extracts used for SNP genotyping were in the range of 20-65 ng μl − 1 .…”

“…Fennoscandia (Norway, Sweden, Finland and Denmark), however, provides unique opportunities to explore fine-scale geographic structure in crops and how it relates to known agrarian history. In Sweden, Finland and Norway, seed collections, compiled by agronomists during the late nineteenth century, mainly to be used as display objects, provide an alternative material to extant landraces (Leino et al, 2009;Leino, 2010). Sampling was carried out 'on farm', and sampling location is frequently detailed down to the specific farmstead.…”

Genetic diversity in local cultivars of garden pea (Pisum sativum L.) conserved ‘on farm’ and in historical collections

“…Markers were chosen to have a high polymorphic information content (PIC) value, be well distributed over the genome, and, to accommodate for the fragmented nature of the DNA in historical seeds, to amplify rather short fragments (less than 400 bp). PCRs were run as described in Leino et al (2009). Amplification products were analysed by capillary gel electrophoresis and confocal laser scanning on a MegaBACE 500 DNA Analysis System (Amersham Biosciences) or an ABI 3130xl Genetic Analyzer (Applied Biosystems, CA, US).…”

Twentieth-century changes in the genetic composition of Swedish field pea metapopulations

“…Thus, the seeds are no longer viable. However, DNA in the aged peas is relatively intact and permits PCR amplification of single-copy nuclear genes (Leino et al, 2009). Collected before the advent of pea breeding, these historical samples offer a snapshot of the genetic diversity present during the height of field pea cultivation in Sweden and constitute a valuable reference material.…”