Apple and Pear cultivar identification by DNA profiling at Aberystwyth University

Aberystwyth University is pleased to be working with The Marcher Apple Network in providing a service for apple and pear cultivar identification through DNA profiling. To have your cultivar identified, please send your fresh tissue samples (leaf, stem or fruit) by first class post in a sealed polythene bag to:

Dr Danny Thorogood
IBERS,
Gogerddan,
Aberystwyth,
SY23 3EE.
Phone: +44 1970 823176
Mobile: +44 7980 919583
e-mail: dnt@aber.ac.uk

Please also include your name and address and telephone and e-mail contact details. Invoices for £23 + VAT will be sent to you after you have been notified of the successful identity of your cultivar in a brief report. It is helpful if you can contact Dr Thorogood before sending samples to ensure that when samples arrive they are freeze-dried immediately and stored in readiness for DNA extraction. If there is more than one sample included, remember to clearly label your individual samples.

Methodology

Sufficient quantities of DNA for successful PCR can be extracted from a range of live tissue samples such as green leaves, fruit at any stage of development including ripe stored fruit, stem and bud tissue including dormant plant material. This means that identification can be made at any time of the year.

DNA profiling is done using twelve microsatellite (simple sequence repeat) markers developed as a set of European standards for apple cultivar identification. DNA extraction is made using a Quiagen DNAeasy plant mini kit and after appropriate dilutions and PCR, using multiplexed fluorescent dye-labelled primers, DNA is subjected to capillary electrophoresis using an ABI 3730 DNA Analyzer (Applied Biosystems). Allele calls are made using Genemapper v3.7 software and adjusted to align with allele calls according to a set of DNA samples from known cultivars provided by Dr Matthew Ordidge, National Fruit Collection Curator at Reading University, run on the IBERS’ ABI 3730 DNA Analyzer machine. Cultivar identification is done by screening sample profiles against the current version of FruitID’s Fingerprint Explorer – SSR Malus MS Excel spreadsheet developed by Mr Peter Laws. The spreadsheet contains more than 3000 apple varieties including the complete Brogdale National Fruit Collection and cultivars already screened through the Register of Local Cultivars scheme.

Terms and Conditions

We are confident that the identifications you receive are accurate and reflect the genotypic identity of the tissue samples provided. Note however that slight variants of the known variety (often called ‘sports’) may exist. These are created by vegetative mutations in tiny parts of the genome of the plant (often single genes). These mutations may have profound effects on the variety’s characteristics even though they essentially maintain the vast majority of the originator plant’s genetic make-up. A classic and very common variant of the Bramley’s Seedling is the Crimson Bramley, which, as you’d expect, produces fruit that is significantly redder than its progenitor variety. The DNA profiling data that we collect will not be able to distinguish these variants. Morphological analysis could be carried out in order to distinguish these. With further development of so-called next-generation sequencing (NGS) technologies it may be possible to carry out genetic tests within the scope of the average household budget to screen for such mutant forms.

We will provide you with your fruit cultivar identity in a report that will include the raw DNA profile data. The data is kept by us as a confidential reference. You may wish to submit an unmatched variety for consideration to be named and registered on the list of the Register of Local Cultivars convened by Peter Laws of FruitID. For further details of this scheme, please refer to the FruitID.com website or contact the Marcher Apple Network. Registration does not imply Plant Breeder’s Rights or indicate any value to the cultivar registered through the scheme.

In the unlikely event that we are unable to process your sample we will contact you and will be happy to receive another sample for analysis at no extra cost.

We aim to identify your sample in the shortest possible time. This is dependent on the number of samples we have to process as it is much more cost efficient to run samples in large batches but you should expect an identification in, at the very most, six months from sample receipt.