Evidence Project Final Report

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2.2 Summary of all marker data available

Marker	Genotype Total (No.)	Genotype Total (%)
ACS1¹
1	945	53
2	141	8
1/2	708	39
Total No. Accessions	1794
ACO1²
1	31	1.7
2	0	0
1/2	1341	74.7
(1>/2)	(382)	(21.3)
(1/<2)	(40)	(2.2)
Total No. Accessions	1794
PG1³
1	176	90.3
2	0	0
1/2	19	9.7
Total No. Accessions	195

¹ACS1-1 and ACS1-2 indicate homozygotes for each allele, ACS1-1/2 indicates heterozygotes;

²ACO1-1 and ACO1-2 indicate homozygotes, ACO1-1/2 indicates a heterozygote and ACO1-1>/2 and ACO1-1/<2 indicates the presumed heterozygotes with uneven scores (as above, the results for this marker were felt to need further study to explain this finding);

³PG1-1 and PG1-2 indicate homozygotes for each allele, PG1-1/2 indicates heterozygotes.

2.3 Primers and conditions used for SSR genotyping of cobnut

Multiplex 1	Multiplex 2	PCR Cycle
CaT B107¹	CaT B503¹	94^oC 5 min	1x
CaT B501¹	CaT B505¹	94^oC 1 min	}28x
CaT B504¹	CaT B507¹	55-50^oC (decreasing 0.5^oC per cycle) 45s
CaC B028²	CaT B508¹	72^oC 1 min
	CaC B020²	60^oC 30 min	1x

¹Boccacci et al., 2005, Molecular Ecology Notes, 5:934-937.

²Bassil et al., 2005, Journal of American Horticultural Science, 130(4):543-549.

2.4 Primers used for SSR genotyping of cherry

Multiplex 1	Multiplex 2	Multiplex 3	Multiplex 4
EMPaS02¹	BPPCT037³	CPPCT022⁴	EMPA004⁶
EMPaS10¹	CPPCT006⁴	EMPas06¹	EMPA005⁶
EMPaS12¹	PceGA34⁵	EMPaS14¹	EMPA015⁶
UDP98-412²	EMPA002⁶	EMPA017⁶	EMPA018⁶
			EMPA003⁶

¹Vaughan and Russell, 2004, Molecular Ecology Notes, 4:429-431.

²Testolin et al., 2000, Genome, 43:512-520.

³Dirlewanger et al., 2002, Theoretical and Applied Genetics, 105:127-138.

⁴Aranzana et al., 2002, Plant Breeding, 121:87-92.

⁵Downey and Iezzoni, 2000, Journal of American Horticultural Science, 125(1):76-80.

⁶Clarke and Tobutt, 2003, Molecular Ecology Notes, 3:578-580.
PCR conditions were as above, but annealing at 55^oC throughout.

2.5 Accessions scored as flowering time standards

Tree	Accession	Tree	Accession
Apple
17_37	Alkmene	49_19	Idared (LA)
33_37	Blenheim Orange (added 2005)	14_3	James Grieve (LA)
34_73	Braeburn	28_31	Jerseymac
41_105	Bramley's Seedling	27_61	Jonagold 78A
15_37	Cox's Orange Pippin (LA)	14_21	Katja (Katy)
16_59	Cox's Orange Pippin (Wisley)	24_31	Lord Derby
50_61	Crawley Beauty	23_37	Malling Kent
48_5	Delcorf	18_97	Meridian
12_23	Discovery (LA)	49_5	Mutsu (Crispin) (LA)
49_69	Edward VII	16_53	Queen Cox (EMLA)
28_13	Egremont Russet (EMLA)	8_3	Red Astrachan
42_35	Elstar	32_17	Red Charles Ross
25_47	Falstaff	45_51	Royal Gala (Tenroy)
49_61	Feuillemorte	20_109	Saturn
29_33	Fiesta	54_9	Spartan (LA)
45_49	Gala (LA)	8_9	Stark's Earliest
14_37	Golden Delicious (EMLA)	31_1	St. Edmund's Pippin
28_19	Greensleeves	19_5	Vista Bella
5_15	Grenadier (LA)	16_21	Worcester Pearmain (LA)
42_79	Howgate Wonder (LA)
Pear
7_27	Beurre Hardy	9_33	Glou Morceau
12_23	Beurre Superfin	20_23	Louise Bonne of Jersey
19_3	Clapp's Favourite	25_17	Nouveau Poiteau
11_39	Concorde	12_E	Packham's Triumph
9_17	Conference	5_7	Precoce de Trevoux
2_19	Doyenne du Comice	16_7	William's Bon-Chretien
6_19	Durondeau
Plum
6_5	Avalon	21_5	Giant Prune (EMLA)
2_3	Burrell's Red Myrobalan	24_13	Laxton's Cropper (EMLA)
18_9	Cambridge Gage	22_17	Marjorie's Seedling
11_23	Czar (EMLA)	16_3	Oullin's Gage (EMLA)
23_5	Damson Farleigh	16_5	Pershore Yellow Egg
22_19	Damson Prune (EMLA)	8_1	Victoria (EMLA)
17_1	Denniston's Superb	29_1	Warwickshire Drooper
2_15	Early Laxton (EMLA)	23_23	Wyedale
4_15	Early Rivers (EMLA)	5_15	Yellow Cherry Plum
14_13	Excalibur
Cherry
15_13	Bradbourne Black	11_17	Merton Bigarreau
19_1	Colney	7_23	Merton Glory
1_17	Early Rivers	9_19	Napoleon
7_9	Hertford	5_5	Roundel (EMLA)
23_7	Kentish Morello	17_9	Stella
15_3	Lapins	17_17	Sunburst
7_13	Merchant	15_11	Van
Quince
3_G	Ludovic	9_G	Vranja
Apricot
1_1	Alfred	1_7	Farmingdale
1_5	Early Moorpark

3. Records and Archives

A website was established, specifically to make the NFC database publically available (www.nationalfruitcollection.org.uk). Prior to this contract, the digital NFC data had been held in a number of different places and formats: key accession details (detailing the origin of the specific accessions in the collection) along with a range of variety specific data from the digitisation of the National Apple Register (Smith, 1971) were held in a Microsoft Access database which was not publically accessible; further details, including general descriptive information about the varieties which the accessions represent, were held alongside the standard photographic images of accessions and flowering time data on the Brogdale Horticultural Trust website (although none of these were searchable); further characterisation data gathered during the verification process were held in a range of spreadsheets (although, whilst data were backed up in hard copy in the archive, some digitised data had been lost at the time of transfer). In addition to this, the working catalogue for the collections was held as a spreadsheet which was updated independently to the Access database. To create a more efficient and co-ordinated system, our approach was to bring all data, as far as possible, into a single web based My-SQL database;
As a consequence of the lack of linkage in the original data, a number of inconsistencies were found in the naming or numbering of specific accessions when the files were brought together (individual accession numbers had been allocated retrospectively by the previous curators, based on the records of accession of varieties at Brogdale, but these had occasionally been subject to later change based on new findings around the provenance of the current tree [especially where there had been multiple accessions for a given variety]). These inconsistencies were addressed through bringing the Access database together with the spreadsheet based catalogue and data (Milestone 2), allowing the NFC database to differentiate where data belonged to the current, rather than a previous accession, and to correctly align with the situation in the field, in cases where accessions had been deaccessed, lost and/or re-accessed under a new number. The database was made publically available from an early stage (Milestones 4 and 8);
Fewer digitised data sets were available than was expected at the start of the project and additional data were consequently digitised for inclusion in the database; these included descriptive data generated during verification of the Cherry and Pear collections. Additionally, raw data used to generate 10-year flowering time means were digitised as it was apparent that these contained further, useful details for understanding the seasonal, and climatic variations in flowering time. Further data collected through the ongoing verification process and through monitoring of flowering time were also added to the database;
Pre-existing characterisation data for the apple collection were standardised where possible to align with the ECPGR standardised descriptors (IBPGR/CEC 1982, and currently in updated draft form). Whilst the ECPGR descriptors themselves had been used as a basis for the verification process, the data recorded often quoted multiple, or concatenated descriptors in an attempt to include the variation within the biological sample (and to allow for the subjectivity of the descriptors). Many of the other data included in the verification records were taken directly from the National Apple Register (Smith 1971) as this had been accepted as a record of the historical verification of the accessions in cases where the material was held at Brogdale at the time of writing. However, the National Apple Register contains descriptions both from Brogdale (although made before the ECPGR recommendations) and from the published literature, and the consequence of this was that these descriptions included a much wider set of descriptors than the ECPGR standards, or than were suitable for use in a workable search tool (for example, 141 ‘unique’ descriptors were included for ground colour [including ‘whitish green’, ‘pale green’, ‘pale greenish white’, ‘whitish green/green’ and ‘whitish/green’ amongst others] where the updated draft ECPGR set allows for Yellow, Whitish yellow, Green yellow, Whitish green, Green, Orange, or Red. Similarly, 405 ‘unique’ descriptors had been used for shape). Having standardised these data, new search protocols were able to be developed (Milestone 25) to make the data considerably more accessible to users (Milestone 10); to clarify the original source, the data were also individually referenced to either the NFC archives or the National Apple Register in the database;
Numerous images of fruit on the tree and blossom had been taken during the previous contract but had not been processed for inclusion in the database. Over 6,000 images of fruit or blossom were screened to select approximately 1,800 for inclusion in the database; a further 333 images of cherry and plum fruit were also identified for inclusion. Additional studio images were taken in a standard format and/or processed for inclusion and 468 further studio images were added to the database. A further 323 images of fruit on the tree were taken in the apple and pear collections for inclusion. A summary of the current status of the image collection in the database is included in 3.2;
A name checking tool was developed within the database. This was produced initially in line with the aims of ECPGR, where it has been identified that many collections hold matching accessions under different local names, some of which will be recognised within the National Apple Register list of synonyms and some of which will not. The tool is able to check a given list of accession names against approximately 23K names in the database and either identify uniquely recognised names/synonyms, or highlight homonyms (where names have historically been used for more than one variety, as either an accepted name or synonymously), or alternatively, to allow the user to propose and align their new synonyms or local names with existing accepted names. This tool was used in the alignment of the other UK collections (described further below) to the NFC data and was demonstrated and utilised at the ECPGR Malus/Pyrus meeting in Weggis (2012);
Other additions to the database included creating links between related accessions based on shared parentage, so that users can access details of offspring or parental varieties in the collection, as well as clonal information, to link accessions with their clones or sports. Accessions were also linked based on shared periods of flowering. Accession and deaccession notices have been added to the website to highlight new or outgoing material (Milestone 27).
Full lists of accessions were supplied and included in the UK National Plant Inventory on a regular basis (with kind help from colleagues at the University of Aberystwyth) and these were subsequently used to update the EURISCO database. Full accession lists and descriptive data were also supplied to the Fera Plant Varieties and Seeds team in line with the need to develop a UK national list of fruit varieties. Data were also supplied to Plant Heritage to aid with their assessment of the status of cultivated varieties as part of their Threatened Plants Project. Full listings of names were supplied to the RHS for use by their taxonomy team and both accession names and descriptive data were made available and utilised in the EU FruitBreedomics project. In addition, various smaller sets of data and information were supplied on a regular basis in response to requests from researchers, nurserymen, horticultural groups and the public (although these were too numerous to detail);
Collection listings were processed for a number of other significant UK collections with a view to their inclusion in the NFC database. The aim of this was to develop the NFC database as a more inclusive database for the fruit tree genetic resources held in collections within the UK, to allow us to recognise where material from additional varieties was held, as well as monitoring where accessions in the NFC may effectively be backed up in other collections. Initially, this was started with the inclusion of listings from the Plant Heritage National Plant Collection™ of Perry Pears at Hartpury.
The hard copy paper archives and library at Brogdale were in need of assessment at the start of the project. The archive/library contained a combination of materials, many of which had been left over from the time when Brogdale was an experimental horticulture station (Brogdale EHS). During transfer from the previous contract, carried out by the Brogdale Horticultural Trust, there had been a lack of clarity on which material should be strictly the responsibility of the NFC and a process of rationalisation of the library was therefore carried out. A number of long unbound runs of trade magazines and journals, of little direct relevance to NFC, along with extensively replicated reports and leaflets (accrued in the time of Brogdale EHS) were disposed of with a view to focussing the archive on material which was of relevance to the current collections and had potential value as a resource at Brogdale.

Further details relating to the above are summarised below (with additional detail included in annual reports):

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