wp 6 database improvement and enrichment leading partner : jki germany, e. maul second annual...
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WP 6 Database improvement and enrichment Leading partner : JKI Germany, E. Maul
Second Annual Workshop of GrapeGen06
Gödöllő, Hungary – 8th to 10th July 2008
Council Regulation (EC) N°870/2004 AGRI GEN RES #008
GrapeGen06
Storage and retrieval of • MCPD-data • ampelographic descriptor data• photos• SSR-marker data• On-farm maintenance• Vitis sylvestris preservation• Trueness to type ascertainment
Establishment of a procedure for a continuous follow up even after termination of the project
Genetic resources management and monitoring
The European Vitis Database (www.eu-vitis.de)
Short to medium term objectives:
The European Vitis Database (www.eu-vitis.de)
• Quick search - (MCPD)• Advanced search - (MCPD, descriptor data are not yet available) • Photo search
Achievements until June 2008:
Public access
Descriptors
Links
Tabular listing:
- Status quo and future options of the database
The European Vitis Database (www.eu-vitis.de)
The European Vitis Database (www.eu-vitis.de)
European Fruit Databases: contents and data retrieval(ECPGR fruit database managers meeting, 23 June, Gembloux, Belgium)
Objective: sharing of competence and modules
Contents and search options Vitis Malus Prunus Pyrus
Access levels web site:Public search x xAll partner access x-1 xPartner specific access x-1Private access for DB-manager (Internet) xPrivate access for DB-manager (local) x-1
MCPD's employed: partiel x xcomplete FAO/IPGRI -EURISCO descriptors x xCrop specific descriptors x xAEGIS descriptors xMCPD excel file for download x
MCPD-data search options:Quick search x xAdvanced search x x
x stands for: task achievedx-1 stands for: implementation intended in 2008
The European Vitis Database (www.eu-vitis.de)
European Fruit Databases: contents and data retrieval(ECPGR fruit database managers meeting, 23 June, Gembloux, Belgium)
Objective: sharing of competence and modules
Contents and search options Vitis Malus Prunus PyrusCharacterisation:Descriptors x xDescriptor excel file for download x
Characterisation data: Search option (static or dynamic search function) x-1
SSR-marker:Descriptors x
SSR-marker data:Search option (Static or dynamic search function) x-1
Photos:Search xGallery x-1
x stands for: task achievedx-1 stands for: implementation intended in 2008
The European Vitis Database (www.eu-vitis.de)
European Fruit Databases: contents and data retrieval(ECPGR fruit database managers meeting, 23 June, Gembloux, Belgium)
Objective: sharing of competence and modules
Contents and search options Vitis Malus Prunus PyrusFuture functionalities:Download (xls, csv, xml-format):MCPD data x-1 xDescriptor data x-1 xSSR-marker data x-1
Print view x-1 x
Upload of data files:MCPD data x-1Descriptor data x-1SSR-marker data x-1
On-line working:Addition x-1Modification x-1Deletion x-1Log-book x-1
x stands for: task achievedx-1 stands for: implementation intended in 2008
Advanced search: characterization and evaluation data
Ampelographic data200720082008etc.
SSR-markerdata20082008etc.
The European Vitis Database (www.eu-vitis.de)
Exportation of the data
• Passport data• Characterisation data• SSR-marker data
Photos
XXetc.
OIV Code N° descriptor notation
OIV 001 Young shoot: shape of the tip 7=openedOIV 003 Young shoot: intensity of anthocyanin coloration on
prostrate hairs of the shoot tip1=none or very low
OIV 004 Young shoot: density of prostrate hairs of the tip 5=mediumOIV 006 Shoot: attitude (before tying) 7=semi droopingOIV 007 Shoot: color of dorsal side of internodes 1=greenOIV 008 Shoot: color of the ventral side of internodes 2=green OIV 015 - 1 Shoot: distribution of anthocyanin coloration on the
bud scales2=basal
OIV 015 - 2 Shoot: intensity of anthocyanin coloration on the bud scales
3=weak
OIV 016 Shoot: number of consecutive tendrils 1=2 or lessOIV 051 Young leaf: color of the upper side (leaf 4) 3=bronzeOIV 054 Young leaf: density of erect hairs between main
veins on the lower side of blade (4th leaf )
7=high
OIV 067 Mature leaf: shape of blade 2=wedge-shapedOIV 068 Mature leaf: number of lobes 3=fiveOIV 070 Mature leaf: area of anthocyanin coloration of main
veins on upper side of blade3=up to the 1st bifurcation
OIV 074 Mature leaf: profile 1=flatOIV 075 Mature leaf: blistering of upper side of blade 1=absent or very weak
Advanced search: characterization and evaluation data
The European Vitis Database (www.eu-vitis.de)
AccenameColor of berry skinCultivar nameHolding institutionAccession numberSpecies Country of origin of the cultivarYear of observation
The European Vitis Database (www.eu-vitis.de)
Summary of applications intended to be developed until the end of 2008:
• Set up of 3 different access levels (public access, all partner access and partner specific access)
• Search function for descriptor data
• Development of modules enabling partner specific modification of data records: addition, updating and deletion of single records
• Uploading of data files
• Downloading of records
• Development of a log book documenting the user activities, encompassing user id, update-time and summarizing the intervention
• Photo gallery
The European Vitis Database (www.eu-vitis.de)
Additional programming work to be arried out:
GrapeGen06 specific modules:
• On-farm maintenance• Vitis sylvestris preservation• Trueness to type ascertainment
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
The European Vitis Database (www.eu-vitis.de)
Multi crop passport descriptor data
Ampelographic descriptor data
Photos SSR-marker data
On farm data
Location dataGenotype data
Vitis vinifera subsp. sylvestris data
Population dataGenotype data
Importance of the accession number:
Trueness to type ascertainement
Key field = accession number
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
Presentation of participating institutes as in Genres#081
Partners of Genres#081: verification of additional informationNew partners within GrapeGen06: transmisson of additional information
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
The European Vitis Database (www.eu-vitis.de)
Static search form
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
Sorting out of collections: assignment of accession names to cultivar names
Proposition of a table comprising the following criteria:
Accession number Accession nameCultivar name Cultivar numberTrueness to typeConfirmation by ampelographyConfirmation by SSR-markersConfirmation by bibliography (no)Bibliography (volume)Bibliography (page)
The European Vitis Database (www.eu-vitis.de)
Discussion:
- MCPD-lists? Encountered difficulties
- Importance of a unique accession number
- Partner contact data, expertise
- Descriptor data: static or dynamic search?
- Cultivar name, accession name and synonyms. How to sort out collections respectively the database and to assign cultivar names?
- Layout, functionality etc. of the database
- Photo gallery necessary?
The European Vitis Database (www.eu-vitis.de)
Deadline: before September 30, 2008Sending of partner specific information and passport data in the MCPD Format
Deadline: before November 30, 2008Sending of WP1 – WP5 data
WP 6: 2nd year activities
The European Vitis Database (www.eu-vitis.de)
Deadline: before December 31, 2008Accomplishment of the most important database applications (MCPD and characterisation data, on-line working)
1 2 3 4 5 6 7TRUENESS_TO_TYPE INSTCODE ACCENUMB COLLNUMB COLLCODE GENUS SPECIES SPAUTHOR
yes DEU098 DEU98-1993-296 Vitis vinifera L.not checked DEU098 DEU98-2001-075 Vitis vinifera L.not checked DEU098 DEU98-2001-076 Vitis vinifera L.not checked DEU098 DEU98-2001-077 Vitis vinifera L.not checked DEU098 DEU98-2001-078 Vitis vinifera L.not checked DEU098 DEU98-2001-079 Vitis vinifera L.
yes DEU098 DEU98-1993-297 Vitis vinifera L.not checked DEU098 DEU98-2001-080 Vitis vinifera L.not checked DEU098 DEU98-2001-121 Vitis vinifera L.
FAO / IPGRI MULTI-CROP PASSPORT DESCRIPTORS
Passport data
0 - TRUENESS_TO_TYPEyes, no, not checked
1 - INSTCODE (Institute code)Example: GRC051
2 - ACCENUMB (Accession number)Example: DEU098-1993-296
3 - COLLNUMB
4 - COLLCODE
5 - GENUS. Example : Vitis
6 - SPECIESExample : vinifera
7 - SPAUTHORExample: L.
8 9 10 11 12SUBTAXA SUBTAUTHOR CROPNAME ACCENAME ACQDATE
var. wine grape ARBST BLAU 1993var. OESTERREICHISCH WEISS 2001var. wine grape VELTLINER BRAUN 2001var. wine grape VELTLINER GRAU 2001var. wine grape VELTLINER ROT 2001var. wine grape TROYEN 2001var. wine grape ARBST BLAU 1993var. wine grape;table grape MADELEINE VIOLET 2001var. FURNER HOTTLINGER 2001
FAO / IPGRI MULTI-CROP PASSPORT DESCRIPTORS
Passport data
8 - SUBTAXAExample: ssp. sylvestris
9 - SUBAUTHOR
10 - CROPNAME (Common crop name – utilization)Wine grape, table grape, raisin grape, rootstock (ornamental grape, wild grape). If multi-use exists, different uses have to be separated by semicolon without spaces.Example: wine grape;table grape
11 - ACCENAME (Accession name)Designation of the accessionExample: Ruländer
12 - ACQDATE (Acquisition date)Date on which the accession entered the collection as YYYYMMDDExample: 1968Example: 20020620
FAO / IPGRI MULTI-CROP PASSPORT DESCRIPTORS
Passport data
13 14 15 16 17 18 19 20 21ORIGCTY COLLSITE LATITUDE LONGITUDE ELEVATION COLLDATE BREDCODE SAMPSTAT ANCEST
300 PINOT NOIR CLONE300300300300300300 PINOT NOIR CLONE300300
13 - ORIGCTY
14 - COLLSITE
15 - LATITUDE
16 - LONGITUDE
17 - ELEVATION
18 - COLLDATE
19 - BREDCODE (Breeding institute code)FAO Institute Code of the institute that has bred the materialExample: AUT024
20 - SAMPSTAT (Biological status of accession)Example: 110) Natural = Vitis vinifera ssp. sylvestrisExample: 300) Traditional cultivar/landrace = Gouais blancExample: 412) Hybrid = Geilweilerhof 3-28-46Example: 500) Advanced/improved cultivar = Rathay
21 - ANCEST (Ancestral data) Example: Pinot x HeunischExample: Pinot noir open pollinationExample: Pinot noir self pollination
FAO / IPGRI MULTI-CROP PASSPORT DESCRIPTORS
Passport data
22 23 24 25 26 27 28 29 30 31COLLSRC DONORCODE DONORNUMB OTHERNUMB DUPLSITE STORGAE REMARKS COLLDESCR BREDDESCR DONORDESCR
40 2040 2040 2040 2040 2040 2040 2040 2040 20
22 - COLLSCR (Collecting/acquisition source) 40) Institute, Experimental station, Research organization, Genebank (most cases)
23 - DONORCODE (Donor institute code)
24 - DONORNUMB (Donor accession number)
25 - OTHERNUMB (Other identification (numbers) associated with the accession)
26 - DUPLSITE (Location of safety duplicates)
27 - STORAGE (Type of germplasm storage) 20) Field collection (most cases)
28 - REMARKS (Remarks)
29 - COLLDESCR (Decoded collecting institute)
30 - BREDDESRC (Decoded breeding institute)
31 - DONORDESCR (Decoded donor institute)
FAO / IPGRI MULTI-CROP PASSPORT DESCRIPTORS
Passport data
32 33 A B C DDUPLDESCR ACCEURL VARIETY NAME BERRY COLOR COUNTRY OF ORIGIN OF THE VARIETY Bredyear
PINOT NOIR N FRAOESTERREICHISCH WEISS B AUT
VELTLINER BRAUN B HUNVELTLINER GRAU G AUTVELTLINER ROT RS ITA
TROYEN N FRAPINOT NOIR N FRA
MADELEINE VIOLET N FRAFURNER HOTTLINGER RG ITA
32 - DUPLDESCR (Decoded safety duplication location)
33 - ACCEURL (Accession URL)
Vitis specific descriptors:
A. Variety NameName of the variety, after it has been identified with certainty Example: Prokupaz
B. Berry colorColor of the berry skin: green, green-grey, green-rose, green-red, green-black, grey, grey-rose, rose, red, red-violet, black, black-red, black-grey Example: green-rose
C. Country of origin of the varietyCode of the country in which the variety originatedExample: ARM
D. BREDYEAR (Year of crossing)Year in which the variety was created as YYYYExample: 1926
Characterization and evaluation data
INTERNATIONAL CODE OF BOTANICAL NOMENCLATURE
(http://ibot.sav.sk/icbn/main.htm)
DIVISION II. RULES AND RECOMMENDATIONS CHAPTER VII. ORTHOGRAPHY AND GENDER OF NAMES SECTION 1. ORTHOGRAPHY
Article 60
60.1. The original spelling of a name or epithet is to be retained, except for the correction of typographical or orthographical errors and the standardizations imposed by Art. 60.5 (u/v or i/j used interchangeably), 60.6 (diacritical signs and ligatures), 60.8 (compounding forms), 60.9 (hyphens), 60.10 (apostrophes), 60.11 (terminations; see also Art. 32.7), and 60.12 (fungal epithets).
Ex. 1. Retention of original spelling: The generic names Mesembryanthemum L. (1753) and Amaranthus L. (1753) were deliberately so spelled by Linnaeus and the spelling is not to be altered to "Mesembrianthemum" and "Amarantus", respectively, although these latter forms are philologically preferable (see Bull. Misc. Inform. Kew 1928: 113, 287. 1928). - Phoradendron Nutt. (1848) is not to be altered to "Phoradendrum". - Triaspis mozambica A. Juss. (1843) is not to be altered to "T. mossambica", as in Engler (Pflanzenw. Ost-Afrikas C: 232. 1895). - Alyxia ceylanica Wight (1848) is not to be altered to "A. zeylanica", as in Trimen (Handb. Fl. Ceylon 3: 127. 1895). - Fagus sylvatica L. (1753) is not to be altered to "F. silvatica". The classical spelling silvatica is recommended for adoption in the case of a new name (Rec. 60E), but the mediaeval spelling sylvatica is not an orthographical error. - Scirpus cespitosus L. (1753) is not to be altered to "S. caespitosus".
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