Quality indicators for passport data in ex situ genebanks

2011 ◽  
Vol 9 (3) ◽  
pp. 478-485 ◽  
Author(s):  
Theo van Hintum ◽  
Frank Menting ◽  
Elisabeth van Strien

Given the increasing importance of data quality for the ex situ conservation and utilization of plant genetic resources (PGR), an indicator was created that quantifies the level of completeness of passport data. This passport data completeness index (PDCI) uses the presence or absence of data points in the documentation of a genebank accession, taking into account the presence or value of other data points. For example, a wild accession should have a well-defined collection site but no variety name. Any type of accession, wild, landrace, breeding material or modern variety, can attain a maximal score of ten for this index. The applicability of this index was tested on the complete contents of EURISCO, the European catalogue of ex situ maintained PGR containing over one million records. Analysis of the PDCI of the material in EURISCO provided valuable insight in the data quality of European collections. The PDCI can be used to identify datasets that might need additional attention and improvement or datasets that need more careful interpretation than others.

Author(s):  
Markus Oppermann ◽  
Stephan Weise

In the wide-ranging field of biodiversity conservation, genebanks play a major role in the preservation of cultivated plants. An important focus of genebanks is the comprehensive documentation of the maintained material. This is a prerequisite to enable users to select the most suitable material for e.g. research or breeding programs (Hoisington et al. 1999). The German Federal ex situ Genebank for Agricultural and Horticultural Crops, which is being hosted at IPK, is the largest genebank in Western Europe. Within the multitude of data associated with plant material (e.g. from various -omics areas or conservation management), the so-called passport data represent the most original and oldest data in genebanks. These metadata are often subject to heterogeneity due to historically different collection and curation, especially if they were received from different institutions around the world. This leads to difficulties in handling these data and can result in misinterpretations. In addition, there are correlations between the individual attributes of the passport data which can lead to a different importance of the individual data points for the users. Major challenges for users are to estimate completeness, correctness and reliability of these data. Thus, it is necessary to assess the quality of these data by defining a suitable set of metrics. Unfortunately, classical data quality measurement metrics, e.g. (Klier 2008), are not sufficient to fulfill the users' needs. Depending on the intention of the user, a different focus is placed on the data. Moreover, the individual attributes of the respective areas can be related to each other. Therefore, a single index value for estimating the quality of a passport record is not sufficient. Rather, it seems to be more promising to generate more differentiated quality statements. We are working on a metrics system that is sensitive to the users' focus. Through a practical set of rules of data quality metrics for accession-related data, the user will be able to influence the weighting of individual domains (e.g. geographical origin, biological status) according to their context (fit-for-use index). The presentation will discuss the background and will give an overview of the progress of this research activity.


2010 ◽  
Vol 8 (2) ◽  
pp. 182-188 ◽  
Author(s):  
Theo van Hintum ◽  
Helmut Knüpffer

Taxonomy plays an essential role in genebank documentation. It is often the first level at which users search material, and it determines the protocols used in the management of collections. Especially, when plant genetic resources information is pooled in systems such as EURISCO, the European catalogue of ex situ plant genetic resources, problems regarding technical handling of taxonomic nomenclature, such as lack of standardization and low quality of data, become apparent. These problems were studied by analysing the content of EURISCO and mapping the taxon names in EURISCO on those used in the United States Department of Agriculture genebank system GRIN-Tax. Thus, the number of spelling errors and the level of standardization could be quantified and improved. An analysis of the content of EURISCO was made, showing a highly unbalanced distribution over crops: 50% of the accessions belong to ten genera only. Mapping EURISCO on the crops listed in Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture showed that 67% of the accessions in EURISCO belong to crops in that list.


2018 ◽  
Vol 2 ◽  
pp. e25223
Author(s):  
Stephan Weise ◽  
Markus Oppermann

The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about more than 1.9 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes in Europe and beyond (Weise et al. 2017). EURISCO, which is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources, is based on a network of National Inventories of 43 member countries. It represents an important effort for the preservation of the world’s agrobiological diversity by providing information about the large genetic diversity kept by the collaborating institutions. Besides the classical passport data, in 2016, EURISCO started to additionally collect phenotypic data about the documented germplasm accessions. The selection of genebank material for both research and breeding purposes is increasingly carried out through the selection of specific phenotypic values, e.g. flowering time or plant height. Thus, these data are of high importance to users of plant genetic resources (PGR) since they determine the value of the respective germplasm. However, because there are no commonly agreed standards existing within the genebank community, this kind of data is very difficult to handle. In this context, the challenges range from synonymous/homonymous descriptor names over different rating scales to different/insufficient amounts of meta information, thus hampering both integration and cross-experiment comparison of data. The presentation will illustrate the approach followed within EURISCO, together with the challenges resulting therefrom. Using this as a solid basis for a discussion about the utilization of this kind of data, the presentation shall be regarded as a call for cooperation.


Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
JS Sung ◽  
CW Jeong ◽  
YY Lee ◽  
HS Lee ◽  
YA Jeon ◽  
...  

2018 ◽  
Vol 6 (11) ◽  
pp. 109-120
Author(s):  
Filomena Rocha

Since the 1970s, Portugal has been endeavouring systematic and coordinated efforts for ex situ conservation of plant genetic resources. Portugal maintains in ex situ a large seed collection of cultivated species (cereals, fibres, grain legumes, vegetables), wild species (forages, MAP species), also national clone collections of olive, fruit trees and grapes. In 2011 the Portuguese National Genebank (BPGV) and ISOPLEXIS implemented the GRIN-Global platform, as provides the opportunity to increase data quality, to have long term sustainability for data curation, integrates all collections in one management system optimizing the costs and staff resources. Now, the main objective in Portugal is to implement the Grin Global Platform at the national level to consolidate its National Programme of Plant Genetic Resources (NPPGR) with all national partners directly involved in the conservation of PGR. The main objectives of this communication are: to demonstrate the valuable contribution of the Grin-Global platform to the NPPGR; discuss the development and status of the Portugal’s National Inventory 2018 in EURISCO, analyse the evolution of the amount of passport information in EURISCO from 2015 to 2018; to address the steps that are being taken in Portugal for the Implementation of the Grin-Global Platform at the national level.


Author(s):  
Paula Bramel ◽  

This chapter reviews the key issues and challenges facing genebanks in preserving crop genetic diversity ex situ. Local crop genetic diversity is challenged with changes in land use, urbanization, land degradation, changes in agricultural practises, availability of improved varieties, changes in market preference, and the impact of climate change. Efforts have been made to secure plant genetic resources ex situ for future use but there are significant issues related to cost effective, efficient, secure, rational, and sustainable long-term ex situ conservation. It begins by addressing issues for the composition of ex situ collections and moves on to discuss issues for routine operations for conservation. The chapter also highlights issues for the use of conserved genetic resources, before concluding with a summary of why the development of sustainable genebank systems is so important.


2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Ines Van den houwe ◽  
Rachel Chase ◽  
Julie Sardos ◽  
Max Ruas ◽  
Els Kempenaers ◽  
...  

AbstractThe CGIAR genebank International Musa Germplasm Transit Centre (ITC) currently holds 1617 banana accessions from 38 countries as an in vitro collection, backed-up by a cryopreserved collection to safeguard global Musa diversity in perpetuity. The ITC also serves as a vital safety backup and transit centre for national banana genebanks and ensures that germplasm is clean of pests and diseases and freely available under the International Treaty on Plant Genetic Resources for Food and Agriculture. In more than 35 years of activity, the ITC has distributed over 18,000 banana accession samples to researchers and farmers in 113 countries. Ex situ conservation of vegetatively-propagated crops such as banana poses very particular challenges. Maintaining the ITC genebank is labor intense and costly. Efficiencies are sought through research and development of techniques on detecting viruses, the genetic integrity of accessions, and on innovative means of safeguarding banana diversity, such as conserving populations of wild species by seed banking. Although the conservation of global banana diversity is the main objective of the ITC, significant value comes from its holistic approach to better understand and promote its germplasm through numerous research activities and resources. Techniques for morphological and molecular characterization serve to identify and describe the collection, while also determining what gaps should be filled by collecting missions with national partners. The evaluation of desirable agronomic traits inherent in Musa spp. are investigated by a high-throughput phenotyping platform, which helps breeding programs to select cultivars resistant or tolerant to biotic and abiotic stresses. Genomic and bioinformatic studies of several banana wild relatives greatly enhance our understanding of Musa genetic diversity, links to important phenotypic traits and bring new methods for management of the collection. Collectively, these research activities produce enormous amounts of data that require curation and dissemination to the public. The two information systems at the ITC, Musa Genebank Management System and the Musa Germplasm Information System, serve to manage the genebank activities and to make public germplasm-related data for over 30 banana collections worldwide, respectively. By implementing the 10-year workplan set out in the Global Strategy for the Conservation and Use of Musa Genetic Resources, the network MusaNet supports Musa researchers and stakeholders, including the ITC, and most importantly, links to the world’s banana-producing countries via three regional banana networks.


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