Genebank Operation in the Arena of Access and Benefit-Sharing Policies

Since the 1990s, the exchange of genetic resources has been increasingly regulated. The Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognize that countries have sovereign rights over their genetic resources and provide a framework for domestic legislations on Access and Benefit-Sharing (ABS). However, within the rules of these international agreements, countries can follow their own interpretations and establish their own rules and regulations, resulting in restricted access to genetic resources and limited benefit-sharing, effects that are contrary to the objectives of these agreements. Although the ITPGRFA’s Multilateral System of Access and Benefit-Sharing provides opportunities for easier access to plant genetic resources for food and agriculture (PGRFA), plant genebanks face increasing complexity in their operation. Adding material to genebank collections has become more difficult, not only because collecting missions need to be negotiated with national and local authorities, but also because acquiring material from other collections is only possible if the origin of the material is properly documented and is done in compliance with regulations. Genebanks may only provide access to their own collections if the material that is to be released is distributed in compliance with a) the conditions under which the material was received and b) the national laws of the country where the genebank is located. The only way genebanks can deal with this new complexity, apart from ceasing to add or distribute material, is by setting up proper procedures to document the origin of every accession and the conditions for their use and further distribution. To prevent a further decrease in access to PGRFA, complexity must be fought. Applying the ITPGRFA’s Standard Material Transfer Agreement (SMTA) only, even for material that does not fall under the ITPGRFA, would simplify matters. The scope of the ITPGRFA could be expanded to include all crops. Furthermore, certain ambiguities (e.g. regarding in situ material and wild species) could be resolved. Finally, compliance with the ITPGRFA should be improved and better monitored.</p

EURISCO: The European search catalogue for plant genetic resources

The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about 1.8 million crop plant accessions preserved by almost 400 institutes in Europe and beyond. EURISCO is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources. It is based on a network of National Inventories of 43 member countries and represents an important effort for the preservation of world's agrobiological diversity by providing information about the large genetic diversity kept by the collaborating collections. Moreover, EURISCO also assists its member countries in fulfilling legal obligations and commitments, e.g. with respect to the International Treaty on Plant Genetic Resources, the Second Global Plan of Action for Plant Genetic Resources for Food and Agriculture of the United Nation's Food and Agriculture Organization, or the Convention on Biological Diversity. EURISCO is accessible at http://eurisco.ecpgr.org

Genetic diversity trends in twentieth century crop cultivars: a meta analysis

In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity

AEGIS, the Virtual European Genebank: Why it is such a good idea, why it is not working and how it could be improved

In this opinion paper, the authors describe the principles of the decentralized European virtual genebank (AEGIS) and analyze the reasons for its lack of success and why the European Cooperative Programme for Plant Genetic Resources (ECPGR) has not been able to improve this situation so far significantly. Possible changes for making AEGIS a success, or at least steps in the right direction, are proposed. These changes center around the creation of a system of certified genebanks with proper quality management, guaranteeing the long-term conservation of, and immediate access to the plant genetic resources conserved in it

The Generation Challenge Programme comparative plant stress-responsive gene catalogue

The Generation Challenge Programme (GCP; www.generationcp.org) has developed an online resource documenting stress-responsive genes comparatively across plant species. This public resource is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. The central objective of this resource is to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). The web-based graphical user interface (GUI) of the resource includes query and visualization tools that allow diverse searches and browsing of the underlying project database. The web interface can be accessed at http://dayhoff.generationcp.org

Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making

Principles for the Inclusion of CWR Data in EURISCO : The principles will promote the creation of CWR national inventories and, for the first time, the transfer to EURISCO of in situ data

In May 2022, a proposal setting the principles for the inclusion of crop wild relative (CWR) data in EURISCO, prepared by Theo van Hintum and José Iriondo, was agreed by the partners of the ECPGR project 'Extension of EURISCO for CWR in situ data and preparation of pilot countries' and the EURISCO Advisory Committee. The agreed principles will promote the creation of CWR national inventories and, for the first time, the transfer to EURISCO of data related to in situ populations of potential importance for breeding and research, and in principle available for users.This project is funded by the German Federal Ministry of Food and Agriculture