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Fingerprinting the National Apple and Pear Collections - GC0140

Description
Defra holds the National Fruit Collections, which are located at Brogdale, Kent, and curated scientifically by Imperial College, London. These collections are not only of heritage interest but constitute valuable genetic resources for projects concerned with the genetic improvement of the UK's principal fruit crops with respect to the requirements of, e.g., sustainable production and climate change. They contain approximately 2200 accessions of apple (Malus) and approximately 545 accessions of pear (Pyrus) - in both cases dessert, culinary, ornamental and cider/perry types - as well as collections of cherry, currant and gooseberry, grape, hazelnut and plum. In recent years, DNA markers known as microsatellites have been developed which are proving very useful for 'fingerprinting' accessions. Such fingerprints are invaluable aids to the management of collections, e.g. when checking for trueness-to-type after propagation or for detecting likely duplicates. In addition, the determination of incompatibility (S) genotype by molecular methods is proving useful for fingerprinting rosaceous tree fruits as well as providing agronomically useful data.

This proposed project, to fingerprint the entire apple collection and to complete the fingerprinting of the pear collection, builds on a successful pilot project to fingerprint the cherry collection and on a current project fingerprinting half of the pear collection, which is in the process of being repropagated. Data from the cherry project has already lead to the confirmation of 42 duplicated accessions and 65 synonyms. Some 90 apple genotypes are also currently being fingerprinted as part of a pilot study by EMR as a sub-contract to Imperial College at Wye. The proposed project will also benefit from decisions to nominate standard microsatellite sets to fingerprint these crops reached at a recent workshop organised by EMR for the ECPGR (European Collaborative Programme for Crop Genetic Resources) and attended by international experts. Moreover, a small complementary project with Imperial College for 2007/08 aims to develop primers for the S locus in apple.

DNA will be extracted from young leaves of the apple accessions and the remaining pears. The DNA extracts will be amplified with a set of ~ twelve microsatellite primers for each crop that have been agreed at the ECPGR workshop. The amplification products will be separated and sized on an automated sequencer. The genotypes will be recorded into an Excel spreadsheet that will be provided to the scientific curator at Imperial College. The data sets will also be submitted to the freely-accessible databases of the ECPGR Malus/Pyrus Working Group. It is expected that some accessions will show amplification patterns indicating triploidy (i.e. three sets of chromosomes) and leaf samples of these will be sent for cytometric analysis to confirm ploidy; again the data will be provided to the scientific curator. Following the initial development work planned with Imperial College, we would also aim to determine the S incompatibility alleles of the apple collection. Such information is of great benefit when selecting pollinator varieties for some of the more unusual accessions in the collection.

The fingerprinting will be a great aid to the efficient management of the collections, as has been demonstrated by the cherry pilot project. It will allow duplicates to be detected, which can lead to rationalisation. And it will provide the reference dataset against which new fingerprints can be checked after repropagation and re-establishment of the collection. The traditional method of doing this, morphological comparison, is time consuming and could take several years during which both the old and new collections would need to be maintained. In addition, because the sets of microsatellites used have been accepted as the standard European set for genotyping, the fingerprints can be compared with those of European collections to aid verification and, potentially, rationalisation at the European level.
Objective
The overall objectives of the project are:

• To use microsatellites to fingerprint the apple accessions in the National Fruit Collection and provide curators with a valuable data set which distinguishes clearly all or most of the varieties tested thus enabling checking of identities and detection of synonyms
• To complete the data set of microsatellite fingerprints of the pear accessions in the National Fruit Collection and provide curators with a valuable data set which distinguishes clearly all or most of the varieties tested thus enabling checking of identities and detection of synonyms

The work will be broken down into the following technical aims:

1. to extract DNA samples from the accessions of the apple collection and the remaining half (275) of the pear collection.
2. to optimise PCR conditions for ~12 informative microsatellite primers in apple, developing multiplexes if appropriate.
3. to determine the microsatellite fingerprints of the accessions of the apple collection and the remaining half of the pear collection.
4. to verify ploidy levels of all accessions which appear from microsatellite analysis not to be diploid.
5. to collate the data into Excel spreadsheets and provide to the scientific curator, e.g. to allow the search for duplicates, to submit the data to the freely-accessible ECPGR Malus and Pyrus databases and to produce papers on ploidy and fingerprinting.
Project Documents
• FRP - Final Report : GC0140 Fingerprinting the National Apple & Pear Collections   (450k)
Time-Scale and Cost
From: 2007

To: 2010

Cost: £319,372
Contractor / Funded Organisations
East Malling Research
Keywords
Allocated - EMR              
Apples              
Horticulture              
Pears              
Plant Genetic Resources              
Science Policy              
Sustainable Farming and Food