Plant Genetic Resources and Databases

Transcription

1 Plant Genetic Resources and Databases Helen Ougham and Ian Thomas IGER's Genetic Resources database - AGRIS 24 The European Central Crop Databases 25 EURISCO and the UK National Inventory 26

2 Helen Ougham and Ian Thomas IGER's Genetic Resources database - AGRIS F or many years, IGER's Genetic Resources Unit (GRU, has been developing a collection of seeds of temperate grasses and legumes. Each seed sample, collected at a particular place and time, is known as an accession. Their origins range from seed donations made by other organisations, through material gathered on collecting trips to other countries (Figure 4.1), to varieties bred at IGER and elsewhere. Each accession is carefully stored under cool, lowhumidity conditions, periodically multiplied to ensure that each batch is available in sufficient quantities, and made available to IGER breeders and researchers and collaborators worldwide. But for seed to be useful, the recipient needs as much information as possible about it - what species? Which country did it come from? What environment was this accession originally growing in? Nowadays, the Internet is the usual means by which such data are made available, so an essential element of the GRU's work is the Aberystwyth Genetic Resources Information System, a database with much additional information associated with it. IGER staff can access it through the Institute's intranet, but it is also available worldwide through the Web. Here, users can find out about collecting activities in the UK and elsewhere, with maps, photographs and details of the species collected. There is information on how seed is produced and stored, and details about our major collaborators. Each accession is described in the database using a series of entries, summarising where it is held, where it originated, what type of accession and - if a b c Number of sites Location: Passo di Casson di Lanza, 20km NW of Pontebbo Description: Alpine pasture grazed by cattle. (Loam rock and sandstone soil) Date: 19/11/1998 Keywords: L. perenne, T. pratensum, T. repens arable arable/grass Freshwater Habitats ditch flush lakeside riverside water-meadow forest deciduous forest coniferous grassland parkland Summary of Species Grasses Semi-natural Genus Species Seed Veg. Seed Veg. Dactylis -glomerata Festuca -gigantea pratensis rubra Lolium multiflorum perenne Legumes Semi-natural Genus Species Seed Veg. Seed Veg. Trifolium pratense repens Figure A collecting trip to Italy, showing species collected, an example of habitat types and a view of a collection site orchard scrub wasteland 24

3 European Cooperative Programme for Crop Genetic Resources Networks ECP GR European Cooperative Programme for Crop Genetic Resources Networks ECP/GR European Central Crop Databases (ECCDB - Lolium - Trifollium repens Figure ECCDB managers Search criteria: Latin name is Lolium sp. 1. ECP/GR Lolium Database collected from its original habitat - the nature and location of that habitat. These data fields were not chosen arbitrarily. They are an extended version of the Multi-crop Passport Descriptors, an international standard developed jointly by the International Plant Genetics Resources Institute (IPGRI) and the Food and Agriculture Organisation. These descriptors are used by the majority of genetic resources groups to ensure that the information they hold about their accessions will be instantly comprehensible to others with whom they exchange it. Although the format is tightly defined, there is scope to add further information in a "Remarks" field, so that special points of interest can be included. All the information in the AGRIS database is available to download in the form of Microsoft Excel spreadsheets, which can also be opened direct from the website: ( welcome/gru/collaboration/agris/download /download.htm). IPGRI The European Central Lolium database is maintained by the Genetic Resources Unit at IGER. The Lolium database is available as a series of downloadable spreadsheets on the internet server of IGER, and is searchable on-line at the Internet server of the Nordic Gene Bank. It contains passport data on 9050 accessions of 15 Lolium taxa stored in 17 European genebanks. The collections contain accessions from 55 countries or regions, 10 of them outside Europe, and include advanced cultivars (2062), primitive cultivars (113), wild or semi-wild material (5171), breeding or research material (317) botanic garden samples (112) and material of unknown type (1275). Seed requests should be sent directly to the holding institutes. Mr Ian D. Thomas Institute of Grassland & Environmental Reseach Plas Gogerddan Aberystwyth Ceredigion, SY23 3EB, Wales, UK Tel: ( ) Fax: ( ) ian.thomas@bbsrc.ac.uk The European Central Crop Databases The international community of those working to conserve plant genetic resources is in constant communication, exchanging seed and information about individual organisations' collections. But it is sometimes difficult and time-consuming to search multiple sources to find stocks and data about a single species. For this reason, the European Cooperative Programme for Crop Genetic Resources Networks, under the aegis of IPGRI, initiated a programme to develop databases which would bring together the information about important crop species conserved in Europe (Figure 4.2). They are called the European Central Crop Databases (ECCDBs), and there are now over 60 of them. Each focuses on a single crop species, or a group of closely-related species. The curator of each database is in contact with all the countries in Europe where collections of his or her species are maintained, usually - but not always - in research institutes, universities or botanic gardens. Ian Thomas at IGER is the curator of two ECCDBs, one for Trifolium repens - white clover - and one for grasses of the 25

4 Lolium peremme L. Enter search values into boxes. Use % sign as wild card. Or select values from the menus Taxonamy Species name Lolium perenne-l Genebank Details Genebank Institute of Grassland & Environmental Research, Genetic Resources Unit, Aberystwyth, Wales Accession Status Collector s Details Collector s Institute Institute of Grassland & Environmental Research, Genetic Resources Unit, Aberystwyth, Wales Collection Date (yyyy mm dd) Collection Number CHEBEL 71:15:1 Location Details Country France Atlas Location Alise Ste Reine Location Alise St. E of Reine Latitude (x dd mm ss) N4733 Longitude (x dd mm ss) E00430 Altitude (m.a.s.l) 330 Aspect (degrees) - Slope (degrees) - Site Relief Summit Figure example of drop-down menu and results of a search of the Lolium database genus Lolium, of which the most agriculturallyimportant are perennial ryegrass and Italian ryegrass. Like AGRIS, the ECCDBs use the FAO/IPGRI passport descriptors. The databases are accessible through IGER's website ( bbsrc.ac.uk/welcome/eccdb/databases/database.htm) and are available to download or open as Microsoft Excel spreadsheets. Many of those who consult the Lolium and Trifolium repens databases, though, are searching for accessions which match specific criteria - for example, material collected from roadside habitats, or from altitudes of more than 1000 metres - and do not need to download the complete dataset. There are therefore drop-down menus which simplify searching, so that the user can easily identify accessions of interest, and, if they wish to obtain seed, find and contact the genebanks where they are conserved (Figure 4.3). EURISCO and the UK National Inventory By no means all germplasm collections throughout Europe are currently represented in the European Central Crop Databases. There are several reasons for this - some species are not crops at all, or not crops of importance in European agriculture; in other cases the collections are simply too small to justify species-specific databases. Yet these collections represent important resources for conserving and making available genetic resources, and maintaining biodiversity. The EU-funded project EPGRIS ( which began in 2000, aims to produce a Europe-wide database - EURISCO. The name is short for European Internet Search Catalogue, and in ancient Greek means "I find". EURISCO is intended to contain information about all the germplasm of all species conserved anywhere in Europe, regardless of whether the plants are originally European or not. As a step towards this, each country will develop a National Inventory of its germplasm, and a National Focal Point has been identified in each of over 40 European countries to carry out this task. Some countries have a single national centre for genetic resources conservation, which naturally acts as the Focal Point. But others, like the UK, maintain their collections at many different sites and store the data in different formats. IGER has been chosen by DEFRA and the UK Plant Genetic Resources Group as the UK's focal point, and Ian Thomas is kept busy receiving data from 18 databases at 14 sites throughout England, Wales and Scotland, and in many cases translating it into the correct format to send on the EURISCO database. Some collections are modest in size - a few hundred accessions - but others are enormous. The Millennium Seed Bank at 26

5 INSTCODE ACCENUMB GENUS SPECIES SPAUTHOR CROPNAME ACQDATE ACCENAME DONORCODE DONORNUMB GBRO Pisum sativum Linnaeus (1753) Pea 1963 PYARA MATAR RUS GBRO Pisum fulvum Sibth. & Sm. Pea 1990 P.FULVUM SWE002 WBH 1787 GBRO Pisum sativum Linnaeus (1753) Pea 1990 WBH 2031 SWE002 WBH 2031 GBRO Pisum fulvum Sibth. & Sm. Pea 1990 P.FULVUM WT 301 GBRO Pisum fulvum Sibth. & Sm. Pea 1990 P.FULVUM WT 304 GBRO Pisum sativum Linnaeus (1753) Pea 1990 HELIA WT 7515 GBRO Pisum sativum Linnaeus (1753) Pea 1990 ENKA WT 7710 GBRO Pisum sativum Linnaeus (1753) Pea 1990 MAZURSKA WT 7712 GBRO Pisum sativum Linnaeus (1753) Pea 1990 KORMONAM WT 9066 GBRO Pisum sativum Linnaeus (1753) Pea 1990 B ARG GBRO Pisum sativum Linnaeus (1753) Pea 1990 KNIGHTS DWARF WHITE ITA004 GBRO Pisum sativum Linnaeus (1753) Pea 1963 MUSNNA RUS GBRO Pisum sativum Linnaeus (1753) Pea 1990 CGN 3352 NLD037 CGN 3027 GBRO Pisum sativum Linnaeus (1753) Pea 1990 GRUNO NLD037 CGN 3027 GBRO Pisum sativum Linnaeus (1753) Pea 1990 MAPLE PEA GBR006 MIS GBRO Pisum sativum Linnaeus (1753) Pea 1991 WANDO GBR GBRO Pisum sativum Linnaeus (1753) Pea 1991 SUGAR GEM GBR GBRO Pisum sativum Linnaeus (1753) Pea 1991 SUGAR LUV GBR GBRO Pisum sativum Linnaeus (1753) Pea 1991 ENGLISH MAPLE GBR006 Ps GBRO Pisum sativum Linnaeus (1753) Pea 1991 ENGLISH MAPLE GBR006 Ps GBRO Pisum sativum Linnaeus (1753) Pea 1991 GIGAS- SWE002 WBH 5879 GBRO Pisum sativum Linnaeus (1753) Pea 1991 ARGENTEUS-arg SWE002 WBH 5406 GBRO Pisum elatius Pea 1962 P.ELATIUS GBRO Pisum sativum Linnaeus (1753) Pea 1991 BONNEVILLE SWE002 WBH 1339 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON FRA043 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON, P2 (NOD-) FRA043 P2 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON, P54 (NOD-) FRA043 P54 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON, P55 (NOD-) FRA043 P55 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON, P56 (NOD-) FRA043 P56 GBRO Pisum sativum Linnaeus (1753) Pea 1991 FRISSON, P57 (NOD-) FRA043 P57 GBRO Pisum sativum Linnaeus (1753) Pea 1991 E135F (sym-13, NOD+FIX-) USA034 E135F GBRO Pisum sativum Linnaeus (1753) Pea 1991 FEW NODULES sym-5 USA034 E2 SPARKLE GBRO Pisum sativum Linnaeus (1753) Pea 1991 SPARKLE USA034 Fig a small part of the UK National Inventory the Royal Botanic Gardens in Kew, for example, contains seed representing over 5000 plant species including about 97% of the UK's natural flora, and the Nottingham Arabidopsis Stock Centre has a staggering 450,000 genetic stocks of the model plant Arabidopsis thaliana (thale cress). When all 18 databases have been incorporated into the UKNI, it will contain information about more than half a million accessions held in UK genebanks, representing a substantial contribution to the EURISCO database. This in turn is part of a worldwide effort to catalogue every country's collections together in a standard format which will be understood by every researcher in the genetic resources area, and so facilitate the vital task of understanding and conserving the biodiversity of the Earth's plant species. Acknowledgements: The EU provides funding to support IGER's participation in the EPGRIS project. Contact: helen.ougham@bbsrc.ac.uk for general information; ian.thomas@bbsrc.ac.uk for seed or details about accessions. 27