scholarly journals Best practices for setting up a repository of phenotypic data for European germplasm holdings

2018 ◽  
Vol 2 ◽  
pp. e25223
Author(s):  
Stephan Weise ◽  
Markus Oppermann
Keyword(s):  
Best Practices ◽  
Genetic Resources ◽  
Rating Scales ◽  
Plant Genetic Resources ◽  
Wild Relatives ◽  
Ex Situ ◽  
Phenotypic Data ◽  
Meta Information ◽  
Passport Data ◽  
Selection Of

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.

scholarly journals Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Maria Y. Gonzalez ◽  
Stephan Weise ◽  
Yusheng Zhao ◽  
Norman Philipp ◽  
Daniel Arend ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phenotypic Diversity ◽  
Spring Barley ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Model Organism ◽  
Ex Situ ◽  
Phenotypic Characterization ◽  
Phenotypic Data ◽  
Seed Regeneration

Abstract The scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federal ex situ Genebank for Agricultural and Horticultural Plant Species. The dataset gathers records for three traits with agronomic relevance: flowering time, plant height and thousand grain weight. This information was collected for seven decades for winter and spring barley during the seed regeneration routine. The curated data represent a source for research on genetics and genomics of adaptive and yield related traits in cereals due to the importance of barley as model organism. This data could be used to predict the performance of non-phenotyped individuals in other collections through genomic prediction. Moreover, the dataset empowers the utilization of phenotypic diversity of genetic resources for crop improvement.

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
Keyword(s):  
Data Quality ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Wild Accession ◽  
Valuable Insight ◽  
Collection Site ◽  
Data Points ◽  
Passport Data

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.

Ex-situ conservation of medicinal plant genetic resources managed by national agrobiodiversity center of Korea

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
JS Sung ◽  
CW Jeong ◽  
YY Lee ◽  
HS Lee ◽  
YA Jeon ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Genetic Resources ◽  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Ex Situ

scholarly journals THE PORTUGUESE NATIONAL INVENTORY ON PLANT GENETIC RESOURCES 2018 - DEVELOPMENT AND STATUS

2018 ◽  
Vol 6 (11) ◽  
pp. 109-120
Author(s):  
Filomena Rocha
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
National Level ◽  
Fruit Trees ◽  
Grain Legumes ◽  
Ex Situ ◽  
Seed Collection ◽  
National Inventory ◽  
Cultivated Species ◽  
Global Platform

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.

Key issues facing genebanks in preserving crop genetic diversity ex situ: overview of the range of challenges

2021 ◽  
pp. 139-154
Author(s):  
Paula Bramel ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Cost Effective ◽  
Ex Situ ◽  
Crop Genetic Diversity ◽  
Ex Situ Collections ◽  
Key Issues ◽  
Market Preference ◽  
The Impact

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.

scholarly journals Safeguarding and using global banana diversity: a holistic approach

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Ines Van den houwe ◽  
Rachel Chase ◽  
Julie Sardos ◽  
Max Ruas ◽  
Els Kempenaers ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Holistic Approach ◽  
Global Strategy ◽  
Ex Situ ◽  
Phenotypic Traits ◽  
Research Activities ◽  
Genebank Management

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.

scholarly journals In situ and ex situ conservation gap analyses of crop wild relatives from Malawi

2020 ◽  
Author(s):  
Nolipher Khaki Mponya ◽  
Tembo Chanyenga ◽  
Joana Magos Brehm ◽  
Nigel Maxted
Keyword(s):  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Grid Cells ◽  
Ex Situ Collections ◽  
Minimum Number

Abstract The study analysed the conservation gaps of the priority crop wild relatives (CWR) taxa for Malawi in order to contribute to the development of a harmonized conservation strategy that helps secure the priority CWR under in situ and ex situ. We used taxa distribution modelling, complementarity analysis and ecogeographic land characterization map to analyse spatial diversity and distribution of 123 priority taxa across different adaptive scenarios. We identified areas of observed and predicted richness, the minimum number of protected areas (PAs) that conserve the broadest ecogeographic diversity in situ and the minimum number of grid cells that capture highest diversity outside PAs to recommend the establishment of genetic reserves. We then analysed the representativeness of the conserved ecogeographic diversity of target taxa in ex situ collections to identify ex situ conservation gaps and advise for priority areas for ex situ collections. For the 123 taxa, 70.7% of the total diversity occurs in 36 PAs with 66.8% of the diversity captured in only 10 complementary PAs. Outside PAs, the broadest diversity was conserved in three grid cells of size 5 × 5 km. Fifty-three of 123 taxa have ex situ collections with only three taxa having ex situ collections at the Malawi Plant Genetic Resources Centre. The findings of this study will guide formulation of conservation actions for the priority taxa as well as lobbying for active conservation of the same under in situ and ex situ.

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