WP 6 Database improvement and enrichment Leading partner : JKI Germany, E. Maul

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:

http://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



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





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





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


Advanced search: characterization and evaluation data

Ampelographic data200720082008etc.

SSR-markerdata20082008etc.


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


AccenameColor of berry skinCultivar nameHolding institutionAccession numberSpecies Country of origin of the cultivarYear of observation



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



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?


Discussion:










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:









Presentation of participating institutes as in Genres#081

Partners of Genres#081: verification of additional informationNew partners within GrapeGen06: transmisson of additional information

Discussion:










Static search form

Discussion:









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)


Discussion:









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


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


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


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


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)


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".

Documents

WP 6 Database improvement and enrichment Leading partner : JKI Germany, E. Maul