Crop Genetics
"Using more than 150,000 seed samples from around 800 genera, we at the IPK are investigating the genetic diversity of cultivated and wild plants and the processes that led to their development. We contribute this knowledge to NFDI4Biodiversity. Research needs this diversity of data so that it can master challenges such as climate change."
Uwe Scholz, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
About the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) is dedicated to basic and application-oriented research on crop plants. Its work focuses on the conservation, research and utilization of the genetic diversity of important crop plants. The operation of an ex-situ gene bank plays a central role in this. This gene bank makes it possible to preserve valuable seeds outside their natural habitat in order to maintain genetic diversity. The seeds are carefully stored in glass jars under controlled conditions and are only cultivated when it is necessary to preserve seed quality, for example to ensure germination.
At the IPK, this valuable resource is combined with research approaches in the fields of genome research, molecular plant biology, systems biology, bioinformatics and modeling. The result is an interplay of genetic conservation and innovative research that both deepens our understanding of genetic diversity and opens up new avenues for the breeding and use of cultivated plants.
The Use Case
How we work together in NFDI4Biodiversity
In line with the general aim of the National Research Data Infrastructure (NFDI) to make research results permanent, structured and freely accessible, the IPK is already actively involved in various initiatives. These include participation in the FAIRagro and DataPLANT consortia. In addition to the NFDI4Biodiversity consortium, which promotes both this central idea and genetic diversity in the context of biodiversity, the IPK is also active in the German Network for Bioinformatics Infrastructure (de.NBI). de.NBI provides the NFDI4Biodiversity consortium with the de.NBI cloud for the development of the RDC. This makes the IPK a data center as well as a data and service provider.
The common goal
The aim of the use case is to integrate the biodiversity of the IPK's plant genetic resources (PGR) into the Research Data Commons (RDC) in order to enable analyses with or the networking of this data. In addition, access to tools is also to be enabled and facilitated. In addition to web applications for displaying genotypic and phenotypic data, workflows are also offered that enable the imputation of genotypic data or the genome-wide association of phenotypic to genotypic data.
The focus of these developments is on crops such as wheat, barley, oats and beans. However, the tools and workflows developed can also be used for other species and can therefore also be applied in the broader biodiversity community of NFDI4Biodiversity.
Standardization and processing of phenotypic data
A central role in the preparation of phenotypic data and the further use of plant genetic resources is played by the MIAPPE standard - a guideline that helps users to organize data on plant genetic resources so that they can be used and processed more easily. Some time ago, the IPK developed an easy-to-use program for working with this standard: the MIAPPE Wizard. Researchers can use it to easily create the required information in MIAPPE format. The IPK is also working with other stakeholders on the further development of BrAPI. BrAPI is an interface designed to enable interoperability between different plant breeding databases.
Previous work and next steps
Work is currently continuing on the development of services and workflows and the concept has already been implemented in an initial RDC pilot called MIRA. This service makes it possible to provide phenotypic data structured according to the MIAPPE standard from an Annotated Research Context (ARC) as a BrAPI server. If the data can be retrieved in a standardized way via BrAPI, programmatic access and thus use is simplified. This makes it possible to connect existing or newly developed tools via the interface in further steps.
Further info
Contact
Would you like to find out more about this Use Case? You can find contact persons here.
Use Case manager (NFDI4Biodiversity)
Sarah Fischer (fischer.sarah@fbn-dummerstorf.de)
Use Case partners (IPK)
Uwe Scholz (scholz@ipk-gatersleben.de)
Manuel Feser (feser@ipk-gatersleben.de)
Publications on the subject
On the Way to Plant Data Commons – a Genotyping Use Case (Feser, Manuel; König, Patrick; Fiebig, Anne; Arend, Daniel; Lange, Matthias ; Scholz, Uwe), 2022. Journal of Integrative Bioinformatics: 19(4)20220033, https://doi.org/10.1515/jib-2022-0033
Over the last years it has been observed that the progress in data collection in life science has created increasing demand and opportunities for advanced bioinformatics. This includes data management as well as the individual data analysis and often covers the entire data life cycle. A variety of tools have been developed to store, share, or reuse the data produced in the different domains such as genotyping. Especially imputation, as a subfield of genotyping, requires good Research Data Management (RDM) strategies to enable use and re-use of genotypic data. To aim for sustainable software, it is necessary to develop tools and surrounding ecosystems, which are reusable and maintainable. Reusability in the context of streamlined tools can e.g. be achieved by standardizing the input and output of the different tools and adapting to open and broadly used file formats. By using such established file formats, the tools can also be connected with others, improving the overall interoperability of the software. Finally, it is important to build strong communities that maintain the tools by developing and contributing new features and maintenance updates. In this article, concepts for this will be presented for an imputation service.
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