The ECPGR Prunus Database

Transcription

1 8 th meeting of the ECPGR Prunus Working Group 7-9 September 2010, Forlì, Italy The ECPGR Prunus Database Contribution of data to the EPDB Progress of the EPDB Discussion on further improvement of the Database Emilie Balsemin, Loïck Le Dantec, Thomas Persohn INRA Bordeaux Fruit Research Station (UREF)

2 Once upon a time the EPDB! Originally established at the Nordic Gene Bank in 1983 Maintained by INRA Bordeaux since 1994 EU GEN RES 61 Project ( ) partners provided data on Prunus genetic resources First online version in September 2005, containing 2,708 cherry accessions maintained by 24 institutes from 11 countries

3 Aims and scope European collections of all Prunus species, cultivated stone fruits and their related species as well as the wild ones EPDB portal will provide access to 6 distinct databases Each DB provides passport, characterisation and evaluation data of plant genetic resources Plum DB Peach DB Cherry DB Intersp. Hybrids DB EPDB portal + Apricot DB Almond DB Photo: Copyright Hélène Christmann, INRA

4 1. Passport data EPDB descriptors List of 13 passport descriptors defined d by the ECPGR Prunus WG * Cherry 15 Plum 15 Common Peach EURISCO standardized Multi Crop Apricot Passport Descriptors (FAO-IPGRI) Hybrids 7 15 Almond 2. Phenotypic data Number of descriptors List of characterisation and evaluation descriptors defined by the Prunus WG * + Pictures of tree, fruits, flowers, leaves 3. Molecular data List of descriptors describing both molecular markers (i.e. SSR primer reverse sequence) and genotypes (i.e. 2 allele sizes for diploid species) * Z tt A t l 2002 P ti * Zanetto A. et al., 2002, Prunus genetic resources in Europe ( ), Genetic Resources and Crop Evolution 49:

5 EPDB data Data = list of accessions with some passport data and some characterisation & evaluation data (no molecular data) 1 MS Excel file per species and per institute (or country) Country Nb Institutes Belgium Switzerland Czech Republic Germany Spain France UK Greece Hungary 1 1,345 Israel Nb Accessions Country Nb Institutes Italy 16 1,373 Norway 1 24 Poland Portugal 1 24 Romania Slovakia Slovenia 1 46 Turkey 1 1,053 Ukraine 8 3, countries 59 institutes Nb Accessions 12,756 accessions

6 Inclusion of new data into the current online EPDB 2010 version Cherry database 2005 version 2,708 accessions 24 institutes 11 countries Plum database + MS Excel files per institute or per country MS Excel files per institute or per country 2010 version 5,087 accessions 39 institutes 16 countries 2010 version 3,300 accessions 32 institutes t 16 countries Almond database (incomplete) MS Excel files (EU GEN RES Safenut project) 8 institutes 5 countries 2010 version 133 accessions 8 institutes 5 countries

7 Contribution of data to the current EPDB available on Internet (1/2) nd: no data Country Nb Cherry Plum Total Nb Institutes accessions in EPDB accessions in EPDB * Prunus accessions Belgium (72%) 153 (23%) 676 Switzerland 1 nd 371 (100%) 371 Czech Rep (61%) 128 (24%) 537 Germany (64%) 188 (36%) 526 Spain (17%) 93 (13%) 730 France (26%) 70 (10%) 710 UK (86%) 32 (6%) 538 Greece 2 30 (30%) nd 100 Hungary (16%) 421 (31%) 1,345 Israel 1 49 (8%) 102 (17%) 618 * Plum DB will be available on Internet at the end of 2010 (%): percentage per country (total number of Prunus accessions)

8 Contribution of data to the current EPDB available on Internet (2/2) Country Nb Cherry Plum Total Nb Institutes accessions in EPDB accessions in EPDB * Prunus accessions Italy 16 1,063 (77%) 87 (6%) 1,373 Norway 1 nd 21 (88%) 24 Poland (49%) 127 (50,6%) 251 Portugal 1 24 (100%) nd 24 Romania (19%) 292 (53%) 548 Slovakia 5 43 (33%) 49 (38%) 129 Slovenia 1 nd nd 46 Turkey (19%) 276 (26%) 1,053 Ukraine 8 1,321 (42%) 789 (25%) 3,157 TOTAL 59 5,087 (40%) 3,300 (26%) 12,756 nd: no data * Plum DB will be available on Internet at the end of 2010 (%): percentage per country (total number of Prunus accessions)

9 Inclusion of new data into the current online EPDB 2010 version Cherry database NEW TOOL 2005 version 2,708 accessions 24 institutes 11 countries Plum database + MS Excel files per institute or per country MS Excel files per institute or per country 2010 version 5,087 accessions 39 institutes 16 countries 2010 version 3,300 accessions 32 institutes t 16 countries Almond database (incomplete) MS Excel files (EU GEN RES Safenut project) 8 institutes 5 countries OLD TOOL 2010 version 133 accessions 8 institutes 5 countries

10 The old tool: demonstration D I E T A G R I C U L T U R E E N V I R O N M E N T

11 The new tool 1. The database is based on recent technologies (freely available) MySQL 5.1+ is the database management system Apache 2 is the Web Server PHP is the scripting language 2. Different levels of access Public access to public accessions only Partner access with specific login and password for each partner - Each partner is responsible of its own accessions. The accessions could be public or accessible only to partners - Data of chosen descriptors, e.g. molecular data, could be available only to partners Private access reserved to the database administrator

12 Database Class Diagram

13 The database philosophy ACCESSION_GROUP ACCESSION INDIVIDUAL Passport data MOLECULAR DATA (SSR or SNP) PHENOTYPIC DESCRIPTION (per year)

14 The database philosophy Example: 5 accessions representing Napoleon cherry variety ACCESSION_GROUP Ex: Napoleon variety ACCESSION 1 accession at INRA (FRA) 1 accession at INRA (FRA) 1 accession at JKI (DEU) 1 accession at EMR (UK) 1 accession at CITA(ESP) INDIVIDUAL 2 trees 2 trees 2 trees 2 trees 2 trees MOLECULAR DATA PHENOTYPIC DESCRIPTION (per year) genotyped genotyped (9 SSR) (6 SSR) observed observed in 2008 in 2008 observed in 2005

15 The new tool: demonstration

16 The main functionalities (1/3) 1. Search for information about one or several accessions Using a quick search tool or an advanced search tool 2. Compare accessions maintained at different sites Possibility to compare phenotypic and/or molecular data among several accessions of the same variety Possibility to compare pictures 3. Export data in different output formats - Search results in PDF or tabular formats (.csv) - Molecular data directly compatible for a wide range of software for genetic analysis such as Structure, DARwin, Genetix, and genetic analysis R packages (0-1 matrix or individual/variable id i matrix)

17 The main functionalities (2/3) 4. Use the Accession_Group level to link accessions 2 non-exclusive possibilities, depending on the decision of the Prunus WG: 1) Group accessions sharing the same accession name or synonym names It is not proved that each group is genetically unique (i.e. not checking by molecular data) It helps to solve synonyms problems, to group duplicates (AEGIS) Accession group n 12 Napoleon 1 accession at INRA (FRA) 1 accession 1 accession 1 accession 1 accession at INRA (FRA) at JKI (DEU) at EMR (UK) at CITA(ESP)

18 The main functionalities (3/3) 4. Use the Accession_Group level to link accessions 2 non-exclusive possibilities, depending on the decision of the Prunus WG: 1) Group accessions sharing the same accession name or synonym names 2) Group accessions that are genetically the same, after analysis of phenotypic and molecular data (with a set of molecular markers quantitatively and qualitatively sufficient) Each group is genetically unique Accession group n 12 Napoleon Accession group n 18 Napoleon 1 accession at INRA (FRA) 1 accession 1 accession 1 accession 1 accession at INRA (FRA) at JKI (DEU) at EMR (UK) at CITA(ESP)

19 The upload process 1. Upload data files using tabular format (.csv) A very useful format for uploading simultaneously many data 2. Capture data directly on a dedicated web interface Possibility to add new accessions and/or new data Possibility to edit or delete the data of your own accessions the database administrator is subsequently informed

20 Work plan & further improvements 1. Finish the technical development of the EPDB model tool Actors: INRA team (Thomas Persohn, Emilie Balsemin & Loïck Le Dantec) Deadline: end of 2010 This tool will be tested by CRA W Gembloux (Belgium) and probably This tool will be tested by CRA-W Gembloux (Belgium) and probably adopted by the Pyrus WG to become the ECPGR Pyrus Database

21 Work plan & further improvements 1. Finish the technical development of the EPDB model tool 2. Develop other Prunus databases structures for plum, almond, apricot, peach cultivated species and their related species Actor: Emilie Balsemin Deadline: end of 2010 A new web site will be created with a common EPDB portal and links between crop databases ( bordeaux.inra.fr/...) Plum DB Peach DB Cherry DB Intersp. Hybrids DB EPDB portal + Apricot DB Almond DB

22 Work plan & further improvements 1. Finish the technical development of the EPDB model tool 2. Develop other Prunus databases structures for plum, almond, apricot, peach cultivated species and their related species 3. Include data into the new Prunus databases Actor: Emilie Balsemin and/or partners Deadline: end of 2010 Data: MS Excel files from partners ( old data information will be updated by partners directly using the Web interface) Other option: partners can send updated data files until the end of October Almond DB Apricot DB Peach DB 1,004 accessions 18 institutes 13 countries 1,926 accessions 17 institutes 12 countries 1,334 accessions 15 institutes 10 countries Content of the future databases with not-updated data

23 Inclusion of new data: Analysis of 14 questionnaires about the status of Prunus collection in European country Number of accessions per country that are already included in the current online version of EPDB Country Almond Apricot Cherry Peach Plum Total Austria Denmark Finland France Hungary Italy 0 0 1, ,150 Latvia Norway Rep Srpska & Bosnia Herz Romania Slovakia Sweden Switzerland Turkey

24 Inclusion of new data: Analysis of 14 questionnaires about the status of Prunus collection in European country Additional accessions from the respective National Prunus collections (in blue) that could be potentially included in the EPDB in the future Country Almond Apricot Cherry Peach Plum Total Austria Denmark Finland France ,076 Hungary Italy , ,384 1, ,248 Latvia Norway 0 = 7,130 additional 0 accessions from these countries Prunus 0genetic resources 0 from 0 other countries Rep Srpska & Bosnia Herz. Romania Slovakia Sweden Switzerland Turkey

25 Conclusions A new tool with new functionalities Add/edit/delete dit/d t your own data Compare data and group accessions Data should be the more complete as possible Passport data (for AEGIS and other purposes) Agree a set of minimum obligatory passport p descriptors? To be discussed after AEGIS presentation and during the WG parallel session Characterisation & evaluation data Add new informative descriptors? Quantitative descriptors? To be discussed during the WG parallel session Molecular data Agree a set of molecular markers and the level of access of data?

26 Thanks to Loïck Le Dantec & Thomas Persohn from INRA Thank you for your attention!

27 The ECPGR European Prunus Database (EPDB) - Status in September 2010 Estimated numbers of accessions to be included into the EPDB as of July 2010 (accessions which have already been included in the Cherry Database are shaded) Cherry Plum Peach Apricot Almond Hybrids Country INSTCODE No. Year No. Year No. Year No. Year No. Year No. Year Total per Institute Total per country BEL Belgium BEL BEL Switzerland CHE Czech CZE Republic CZE Germany DEU Spain ESP ESP FRA France FRA FRA United Kingdom GBR Greece GRC GRC Hungary HUN Israel ISR ITA ITA ITA ITA ITA ITA ITA Italy ITA ITA ITA ITA ITA ITA ITA ITA ITA-CRAB

28 The ECPGR European Prunus Database (EPDB) - Status in September 2010 Estimated numbers of accessions to be included into the EPDB as of July 2010 (accessions which have already been included in the Cherry Database are shaded) Cherry Plum Peach Apricot Almond Hybrids Country INSTCODE No. Year No. Year No. Year No. Year No. Year No. Year Total per Institute Total per country Norway NOR Poland POL Portugal PRT ROM ROM ROM Romania ROM ROM ROM ROM-BT ROM-ST SVK SVK Slovakia SVK SVK SVK Slovenia SVN Turkey TUR UKR UKR UKR Ukraine UKR UKR UKR UKR UKR countries institutes INSTCODE = FAO institute code No. = number of accessions Year = last update