EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material
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Published online 3 October 2022 Nucleic Acids Research, 2023, Vol. 51, Database issue D1465–D1469
https://doi.org/10.1093/nar/gkac852
EURISCO update 2023: the European Search
Catalogue for Plant Genetic Resources, a pillar for
documentation of genebank material
Pragna Kotni1 , Theo van Hintum 2
, Lorenzo Maggioni 3
, Markus Oppermann 1
and
Stephan Weise 1,*
1
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland,
Germany, 2 Centre for Genetic Resources, The Netherlands (CGN), Wageningen University & Research,
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Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands and 3 European Cooperative Programme for Plant
Genetic Resources (ECPGR), c/o Alliance of Bioversity International and CIAT, Via di San Domenico 1, 00153
Rome, Italy
Received July 29, 2022; Revised September 13, 2022; Editorial Decision September 16, 2022; Accepted September 23, 2022
ABSTRACT vated plants and their wild relatives in the future, this di-
versity must be preserved. Genebanks play an important
The European Search Catalogue for Plant Genetic role in long-term preservation efforts. There are about 1800
Resources (EURISCO) is a central entry point for in- genebank collections of plant genetic resources for food and
formation on crop plant germplasm accessions from agriculture (PGRFA) worldwide, of which about 625 are in
institutions in Europe and beyond. In total, it provides Europe (9). It is a truism that something can only be used
data on more than two million accessions, making an if one has information about it. The best resource will not
important contribution to unlocking the vast genetic be exploited if it is not well documented, and without data,
diversity that lies deposited in >400 germplasm col- proper genebank management will not be possible (10). In
lections in 43 countries. EURISCO serves as the ref- other words, the better described PGRFA material is, the
erence system for the Plant Genetic Resources Strat- more valuable it is for potential users and the better it can
egy for Europe and represents a significant approach be preserved. In addition to pure management data and in-
formation on the legal status of the material, it is therefore
for documenting and making available the world’s
important to have information that allows users to select
agrobiological diversity. EURISCO is well established the most suitable material for breeding and research pro-
as a resource in this field and forms the basis for a grammes, especially passport data (about identity and ori-
wide range of research projects. In this paper, we gin) and phenotypic characterisations (about traits) of the
present current developments of EURISCO, which is genebank material (11).
accessible at http://eurisco.ecpgr.org. The European Search Catalogue for Plant Genetic
Resources (EURISCO) is an international aggregated
INTRODUCTION database that aims to provide a central entry point for infor-
mation on the large genetic diversity harboured in the col-
Crop plants are the basis of nutrition for humans and
laborating collections. Presently, it contains data on more
farmed animals. However, biodiversity, including the agri-
than two million genebank samples, so-called accessions,
cultural component, is threatened worldwide by various fac-
which are preserved in >400 institutes in Europe and some
tors (1–4). The progressing climate crisis plays a special role
neighbouring countries. EURISCO is maintained on behalf
here (5,6). In particular, rising temperatures, changing pre-
of the European Cooperative Programme for Plant Genetic
cipitation patterns and the increasing frequency of extreme
Resources (ECPGR) and is based on a network of National
weather events are leading to adverse effects, such as de-
Inventory Focal Points, one in each of 43 member coun-
clining crop yields (7). The changes in the environment due
tries. EURISCO has been available online since 2003 and
to the climate crisis are also forcing farmers to grow other
from 2014 the Leibniz Institute of Plant Genetics and Crop
varieties or even other crops, with the danger of losing the
Plant Research (IPK) Gatersleben, Germany, has been re-
old ones. Furthermore, crop related wild species are increas-
sponsible for the operation and further development of the
ingly under threat of disappearance due to these environ-
information system as well as the coordination of the EU-
mental changes (8). In order to combat this genetic ero-
RISCO network of National Inventory Focal Points.
sion and be able to rely on the genetic diversity of culti-
* To whom correspondence should be addressed. Tel: +49 39482 5 744; Fax: +49 39482 5 155; Email: weise@ipk-gatersleben.de
C The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
D1466 Nucleic Acids Research, 2023, Vol. 51, Database issue
SYSTEM OVERVIEW Since the first description of EURISCO in the NAR
database issue 2017 (12), the volume of data has been ex-
The National Inventory Focal Points of the EURISCO
panding continuously. The number of data provider institu-
member countries are responsible for the development and
tions rose from 376 to 402. The number of accessions docu-
maintenance of the National Inventories. These comprise
mented in the system increased by >200 000 (13%), details
of data about the PGRFA collections maintained by local
of which are illustrated in Table 1. During the same period,
curators in these countries under ex situ conditions. The
the number of phenotypic data points increased by 2.2 mil-
data management of these collections is in many cases sup-
lion (500%). This shows that EURISCO is steadily gaining
ported by IT systems that allow data exchange with the Na-
acceptance as a repository of such data. Moreover, data on
tional Inventory Focal Points, which in turn regularly up-
plant genetic resources are not static. Rather, they are con-
date the data in EURISCO (12). The basis for the core of the
tinuously curated and expanded. On average, between 30
data collection (passport data) is the Multi-Crop Passport
and 40 National Inventory datasets are updated each year,
Descriptors standard (MCPD) (13). MCPD is the globally
either in part or in full. These updates include data of on
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recognised standard for the documentation and exchange
average 350 000–400 000 accessions per year. Regular train-
of passport data on plant genetic resources and enables the
ing workshops, organised with the support of ECPGR, are
acquisition of data following a well-defined and legally legit-
held to support the data providers, which aim, among other
imised procedure. Additionally, a EURISCO-specific for-
things, to raise awareness of various aspects of data quality
mat is used for the exchange of phenotypic data. The pro-
and to successively improve it.
cedures for exchanging data with the National Inventory
Stable and unique identifiers are an important prerequi-
Focal Points are well established, but are constantly being
site for the operation of aggregated databases such as EU-
adapted and improved.
RISCO (10), allowing the information in EURISCO to be
EURISCO runs on an Oracle relational database man-
linked easily to information in other data sources, espe-
agement system using its specific technologies like PL/SQL
cially where it concerns genomics and other omics data,
and Oracle Application Express. The database backend in-
that are not included in EURISCO. Digital Object Identi-
cludes a staging area for pre-processing and data cleans-
fiers (DOIs) have established themselves as a quasi-standard
ing (64 tables) as well as performance-optimised database
in the field of plant genetic resources in recent years (14).
structures for the web frontend (48 tables). The >200
Therefore, the increasing acceptance of DOIs is a very posi-
functions and procedures within 23 packages mainly pro-
tive development. In close cooperation with the Secretariat
vide functionalities for data quality assurance, but also for
of the ITPGRFA, EURISCO offers its data providers the
user-specific download options, visualisations and statistics,
service of carrying out the DOI registration of their acces-
among others. A web frontend with a broad range of func-
sions on their behalf. This service is well established, as re-
tions is available for the users of the system. The frontend is
flected in the continuous increase in the number of DOIs.
meant to be user-friendly for any type of the targeted users,
which include plant breeders and researchers, but also farm-
ers, policy makers and other scholars. The web frontend is ENHANCED WEB INTERFACE
developed with Oracle Application Express technology, ver-
sion 21. EURISCO’s central user interface has recently been com-
pletely revised. It offers a variety of ways to find informa-
tion (Figure 1). In addition to various wizard-based stan-
dard searches, indexes of common crop names and taxo-
UPDATED DATABASE CONTENT AND STATISTICS
nomic terms are offered to provide searches at different lev-
Currently, more than two million PGRFA accessions are els. Map-based searches are also possible. The results can
documented in EURISCO. These include major cereal then be narrowed down using further filters, e.g. faceted
grains such as wheat (205 088), barley (126 330) and maize searches (Figure 2). Various data export features allow data
(67 869), pulses such as beans (55 344), peas (38 914) and to be downloaded for later use. In addition to passport data
vetches (29 438), edible oilseed crops such as sunflower searches, wizards offer the possibility to search for pheno-
(7735) and linseed (20 900), tuber crops such as potatoes typic data.
(15 139), accessions of the Brassica complex (35 308), but One feature that should be highlighted is the sophisti-
also a very large research collection of Arabidopsis thaliana, cated taxonomic search in EURISCO. When searching by
a model plant in life sciences (684 967) is included. In taxonomic names, users often face the challenge that differ-
total, the accessions documented in EURISCO comprise ent PGRFA collections follow different taxonomic schools
6737 genera and 45 175 species. 428 160 of the accessions and traditions, resulting in a variety of accepted names and
are part of the Multilateral System of Access and Ben- synonyms. Therefore, a feature was implemented for EU-
efit Sharing (MLS) of the International Treaty on Plant RISCO that automatically maps the scientific names of all
Genetic Resources for Food and Agriculture (ITPGRFA), accessions against different taxonomic repositories repre-
which means that they have been confirmed by the respec- senting different taxonomic opinions. This leads to much
tive countries to be promptly available under standard and more complete result sets. Currently, the mapping is done
internationally agreed benefit sharing conditions. In addi- against GRIN Taxonomy (15) as well as the Mansfeld’s
tion, there are 2.6 million records of phenotypic data from World Database of Agricultural and Horticultural Crops,
more than 3800 experiments conducted on genebank mate- which is based on the Mansfeld’s Encyclopedia of Agricul-
rial. tural and Horticultural Crops (16). The taxonomic searchNucleic Acids Research, 2023, Vol. 51, Database issue D1467
Table 1. PGRFA accessions of the EURISCO database grouped by genus and species. The ten most common genera are broken down in detail. The total
number of accessions per genus is shown in the column ‘Accs. total’. In addition, the figures from the first description of EURISCO in the NAR database
issue 2017 (12) and the percentage change since then are shown
Genus Species No. of accs. Accs. total Weise et al. (2017) Increase
Arabidopsis thaliana 684 967 685 192 669 587 2.33%
others 225
Triticum aestivum 145 483 205 088 147 055 39.46%
(wheat) durum 17 482
turgidum 15 084
monococcum 3624
spelta 3419
dicoccum 1187
aethiopicum 1048
others 17 761
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Hordeum vulgare 116 283 126 330 105 289 19.98%
(barley) spontaneum 6172
others 3875
Zea mays 67 743 67 869 61 932 9.59%
(maize) others 126
Phaseolus vulgaris 50 211 55 344 49 774 11.19%
(garden bean) coccineus 2329
others 2804
Solanum lycopersicum 22 429 53 295 44 400 20.03%
(tomato, potato, eggplant, etc.) tuberosum 15 139
andigenum 2814
melongena 2219
others 10 694
Vitis vinifera 38 295 47 488 28 819 64.78%
(grape) others 9193
Avena sativa 33 838 42 405 29 429 44.09%
(oat) sterilis 2401
byzantina 1988
others 4178
Pisum sativum 37 424 38 914 29 735 30.87%
(pea) others 1490
Malus domestica 32 553 34 558 27 698 24.77%
(apple) others 2005
others 723 029 649 034 11.40%
Total 2 079 512 1 842 752 12.85%
feature was first described in (17) and has been continuously context, it should not go unmentioned that an extension
expanded since then. of EURISCO to include data on in situ crop wild relatives’
Another feature is the uniform search for common crop populations is currently under preparation and will further
names. Thus far, there is no globally accepted controlled vo- strengthen the role of the system.
cabulary for this. As a result, the PGRFA accessions in EU- In addition, work is ongoing to expand EURISCO’s role
RISCO are described with arbitrary crop names or no crop as a repository of phenotypic data on PGRFA accessions.
name at all, which makes a uniform search for accessions of The amount of corresponding data has increased signifi-
a specific crop across all accessions impossible. For this rea- cantly in recent years. Compliance with the criteria defined
son, a mechanism was developed that automatically maps by FAIR (18) is an important goal for today’s research data
all accessions in EURISCO against the crop names used in management. However, the phenotypic data managed in
GRIN (15), regardless of what data, if any, were provided EURISCO cannot fully comply with these criteria. In the
by the National Inventories for ‘crop name’. This makes it genebank community, a major challenge is that there is a
possible to search uniformly across all two million acces- large variety of small, relatively poorly described pheno-
sions and to achieve significantly better matching results. typing datasets. Some of these are several decades old, but
represent important sources for the use of PGRFA mate-
rial and are indispensable against this background. Due to
SUMMARY AND PERSPECTIVES the history of the data, traits and methods used are often
EURISCO’s main task is to provide a central entry point heterogeneous. Thus, an important goal is to achieve full
for information on plant genetic resources maintained ex compliance with MIAPPE (Minimum Information about
situ in participating institutions. This presents an impor- Plant Phenotyping Experiments (19)) in order to improve
tant contribution to opening up a large part of the millions the FAIRness of the data. To further improve access to the
of accessions preserved in germplasm collections worldwide data available in EURISCO, the implementation of Breed-
for research and breeding. In particular, old landraces and ing API (BrAPI) (20) endpoints is being evaluated. More-
crop wild relatives documented in EURISCO can provide over, the various research projects EURISCO is involved in
important contributions to future breeding efforts. In this are used to develop and test further extensions, such as anD1468 Nucleic Acids Research, 2023, Vol. 51, Database issue
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Figure 1. The different search capabilities of EURISCO.
Figure 2. Overview of the EURISCO web interface. (A) The result set of a search query, which can be further narrowed down using facets. (B) A map-based
search. (C) A detailed view of passport and phenotypic data of a selected accession.Nucleic Acids Research, 2023, Vol. 51, Database issue D1469
improved linkage with genetic data. The web interface will density substantially affect ecosystem function despite invariant
continue to be developed in the coming years. richness. Ecol. Lett., 20, 1315–1324.
5. Habibullah,M.S., Din,B.H., Tan,S.H. and Zahid,H. (2022) Impact of
EURISCO is also the European node of the interna- climate change on biodiversity loss: global evidence. Environ. Sci.
tional PGRFA information system Genesys, operated by Pollut. Res., 29, 1073–1086.
the Global Crop Diversity Trust, and provides the passport 6. Scheffers,B.R., Meester,L.D., Bridge,T.C.L., Hoffmann,A.A.,
data of the accessions maintained ex situ. The phenotypic Pandolfi,J.M., Corlett,R.T., Butchart,S.H.M., Pearce-Kelly,P.,
data mentioned above are provided exclusively through EU- Kovacs,K.M., Dudgeon,D. et al. (2016) The broad footprint of
climate change from genes to biomes to people. Science, 354, aaf7671.
RISCO. The same applies to the in situ crop wild relative 7. Qian,B., Jing,Q., Bélanger,G., Shang,J., Huffman,T., Liu,J. and
data that will soon be included in EURISCO. Together with Hoogenboom,G. (2018) Simulated canola yield responses to climate
systems like Genesys or GRIN-Global, EURISCO forms a change and adaptation in Canada. Agron. J., 110, 133–146.
vital component of the global information system (GLIS) 8. Khoury,C.K., Brush,S., Costich,D.E., Curry,H.A., de Haan,S.,
Engels,J.M.M., Guarino,L., Hoban,S., Mercer,K.L., Miller,A.J. et al.
(21). It is expected that EURISCO will remain an impor- (2022) Crop genetic erosion: understanding and responding to loss of
tant resource in the field of plant genetic resources manage- crop diversity. New Phytologist, 233, 84–118.
Downloaded from https://academic.oup.com/nar/article/51/D1/D1465/6746864 by guest on 07 January 2023
ment and use, and will continue to form the basis for a wide 9. Engels,J.M. and Maggioni,L. (2012) AEGIS: A regionally based
range of research projects. Its further strengthening and de- approach to PGR conservation. In: Maxted,N., Dulloo,M.,
velopment has been included among the 2030 targets of the Ford-Lloyd,B., Frese,L., Iriondo,J. and Pinheiro de Carvalho,M.
(eds). Agrobiodiversity Conservation: Securing the Diversity of Crop
Plant Genetic Resources Strategy for Europe (22). Wild Relatives and Landraces. CABI, pp. 321–326.
10. Weise,S., Lohwasser,U. and Oppermann,M. (2020) Document or lose
it – on the importance of information management for genetic
DATA AVAILABILITY resources conservation in genebanks. Plants, 9, 1050.
11. Hoisington,D., Khairallah,M., Reeves,T., Ribaut,J.M., Skovmand,B.,
EURISCO will be continuously maintained and updated, Taba,S. and Warburton,M. (1999) Plant genetic resources: what can
and is publicly accessible at http://eurisco.ecpgr.org. After they contribute toward increased crop productivity?. Proc. Natl.
its launch in 2003 as a product of an EU-funded project, Acad. Sci. U.S.A., 96, 5937–5943.
continuity of funding of EURISCO has been guaranteed in 12. Weise,S., Oppermann,M., Maggioni,L., van Hintum,T. and
the past twenty years with contributions mainly from the Knüpffer,H. (2017) EURISCO: the European search catalogue for
plant genetic resources. Nucleic Acids Res., 45, D1003–D1008.
European countries that are members of ECPGR. 13. Alercia,A., Diulgheroff,S. and Mackay,M. (2015) In: FAO/Bioversity
Multi-Crop Passport Descriptors V.2.1 (MCPD V.2.1). Food and
Agriculture Organization of the United Nations (FAO). Rome, Italy;
ACKNOWLEDGEMENTS Bioversity International, Rome, Italy.
14. Alercia,A., López,F., Sackville Hamilton,N. and Marsella,M. (2018)
The authors wish to thank the network of the EURISCO In: Digital Object Identifiers for Food Crops - Descriptors and
National Inventory Focal Points as well as all institutions Guidelines of the Global Information System. Food and Agriculture
providing data for their hard work and great commitment. Organization of the United Nations (FAO), Rome, Italy.
15. Wiersema,J.H. (1995) Taxonomic information on cultivated plants in
the USDA/ARS Germplasm Resources Information Network
FUNDING (GRIN). Acta Horticulturae, 413, 109–116.
16. Hanelt,P. (2001) Mansfeld’s Encyclopedia of Agricultural and
Development and maintenance of EURISCO: Euro- Horticultural Crops. Springer, Berlin, Heidelberg.
pean Cooperative Programme for Plant Genetic Re- 17. Kreide,S., Oppermann,M. and Weise,S. (2019) Advancement of
sources (ECPGR), Rome, Italy. Funding for open ac- taxonomic searches in the European search catalogue for plant
genetic resources. Plant Genet. Resources: Character. Util, 17,
cess charge: Leibniz Institute of Plant Genetics and Crop 559–561.
Plant Research (IPK) Gatersleben, Germany; Deutsche 18. Wilkinson,M.D., Dumontier,M., Aalbersberg,I.J., Appleton,G.,
Forschungsgemeinschaft (DFG, German Research Foun- Axton,M., Baak,A., Blomberg,N., Boiten,J.W., da Silva Santos,L.B.,
dation) [491250510, in part]. Bourne,P.E. et al. (2016) The FAIR guiding principles for scientific
data management and stewardship. Sci. Data, 3, 160018.
Conflict of interest statement. None declared. 19. Papoutsoglou,E.A., Faria,D., Arend,D., Arnaud,E.,
Athanasiadis,I.N., Chaves,I., Coppens,F., Cornut,G., Costa,B.V.,
Ćwiek Kupczyńska,H. et al. (2020) Enabling reusability of plant
REFERENCES phenomic datasets with MIAPPE 1.1. New Phytologist, 227, 260–273.
1. Eastwood,N., Stubbings,W.A., Abdallah,M.A.A.E., Durance,I., 20. Selby,P., Abbeloos,R., Backlund,J.E., Basterrechea Salido,M.,
Paavola,J., Dallimer,M., Pantel,J.H., Johnson,S., Zhou,J., Bauchet,G., Benites-Alfaro,O.E., Birkett,C., Calaminos,V.C.,
Hosking,J.S. et al. (2022) The Time Machine framework: monitoring Carceller,P., Cornut,G. et al. (2019) BrAPI – an application
and prediction of biodiversity loss. Trends Ecol. Evol., 37, 138–146. programming interface for plant breeding applications.
2. Backhaus,T., Snape,J. and Lazorchak,J. (2012) The impact of Bioinformatics, 35, 4147–4155.
chemical pollution on biodiversity and ecosystem services: the need 21. Shaw,P.D., Weise,S., Obreza,M., Raubach,S., McCouch,S., Kilian,B.
for an improved understanding. Integr. Environ. Assess. Manag., 8, and Werner,P. (2023) Database solutions for genebanks and
575–576. germplasm collections. In: Ghamkhar,K., Williams,W. and
3. Cardinale,B.J., Duffy,J.E., Gonzalez,A., Hooper,D.U., Perrings,C., Brown,A.H.D. (eds). Plant Genetic Resources for the 21st Century –
Venail,P., Narwani,A., Mace,G.M., Tilman,D., Wardle,D.A. et al. The OMICS Era. chapter 16. Apple Academic Press, Palm Bay, FL,
(2012) Biodiversity loss and its impact on humanity. Nature, 486, USA.
59–67. 22. ECPGR (2021) In: Plant Genetic Resources Strategy for Europe.
4. Spaak,J.W., Baert,J.M., Baird,D.J., Eisenhauer,N., Maltby,L., European Cooperative Programme for Plant Genetic Resources,
Pomati,F., Radchuk,V., Rohr,J.R., Van den Brink,P.J. and De Rome, Italy.
Laender,F. (2017) Shifts of community composition and populationYou can also read
