LettuceDB: an integrated multi-omics database for cultivated lettuce.

Crop genomics has advanced rapidly during the past decade, which generated a great abundance of omics data from multi-omics studies. How to utilize the accumulating data becomes a critical and urgent demand in crop science. As an attempt to integrate multi-omics data, we developed a database, LettuceDB (https://db.

Collaboration between Private and Public Genebanks in Conserving and Using Plant Genetic Resources.

Among the most important users of plant genetic resources, conserved predominantly in public genebanks around the world, are public and private plant breeders. Through their breeding efforts, they contribute significantly to global, regional, and local food and nutrition security. Plant breeders need genetic diversity to be able to develop competitive new varieties that are adapted to the changing environmental conditions and suit the needs of consumers.

Critical Review of the Increasing Complexity of Access and Benefit-Sharing Policies of Genetic Resources for Genebank Curators and Plant Breeders-A Public and Private Sector Perspective.

Plant breeders develop competitive, high-yielding, resistant crop varieties that can cope with the challenges of biotic stresses and tolerate abiotic stresses, resulting in nutritious food for consumers worldwide. To achieve this, plant breeders need continuous and easy access to plant genetic resources (PGR) for trait screening, to generate new diversity that can be built into newly improved varieties. International agreements such as the Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognised the sovereign rights of countries over their genetic resources.

EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material.

The European Search Catalogue for Plant Genetic Resources (EURISCO) is a central entry point for information on crop plant germplasm accessions from institutions in Europe and beyond. In total, it provides data on more than two million accessions, making an important contribution to unlocking the vast genetic diversity that lies deposited in >400 germplasm collections in 43 countries. EURISCO serves as the reference system for the Plant Genetic Resources Strategy for Europe and represents a significant approach for documenting and making available the world's agrobiological diversity.

AEGIS, the Virtual European Genebank: Why It Is Such a Good Idea, Why It Is Not Working and How It Could Be Improved.

Europe is very active in terms of conserving plant genetic resources, with hundreds of genebanks and thousands of dedicated people involved. However, the resulting infrastructure is, along with being very expensive, far from efficient and not very reliable. In this opinion paper, the authors describe how this situation arose, and why the European Cooperative Programme for Plant Genetic Resources (ECPGR), the collaborative umbrella organization of the European countries involved, has not been able to improve this situation so far significantly.

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce.

Lettuce (Lactuca sativa) is an important vegetable crop worldwide. Cultivated lettuce is believed to be domesticated from L. serriola; however, its origins and domestication history remain to be elucidated.

Reliable genomic strategies for species classification of plant genetic resources.

Background: To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a conservative variety of 3-Nearest Neighbours and Naive Bayes) We investigated the effects of the number of accessions per species and misclassification rate on classification success, and validated theirs generic value results with three complete datasets.

Results: We found the conservative variety of 3-Nearest Neighbours to be the most reliable classifier when varying species representation and misclassification rate. Through the analysis of the three complete datasets, this finding showed generic value.

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.

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.

Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations.

Dominant and co-dominant molecular markers are routinely used in plant genetic research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A set of 54 diploid sugar beet (Beta vulgaris L.

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.

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.

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.

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.

Generation Challenge Programme (GCP): standards for crop data.

The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop information platform and network to share genetic resources, genomics, and crop improvement information. This system is being designed based on a comprehensive scientific domain object model and associated shared ontology.

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections.

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species.

Molecular markers: tools to improve genebank efficiency.

Possibilities for using molecular markers to improve genebank efficiency are increasingly present thanks to developments in genebanks and developments in molecular genetics. These possibilities relate to all aspects of genebank management: acquisition, maintenance, characterisation and utilisation. However, two pitfalls should be avoided.