The overriding goal of this project is the generation of genomic data along with the corresponding IT infrastructure that will allow for informed and knowledge-based access and utilization of one of the largest barley collections worldwide. This will set the stage for the Federal ex-situ Genebank to develop from a pure conservation facility, internationally renowned for its technical standards, into a one stop shop for facilitated and informed utilization of crop plant biodiversity.
We aim to (i) implement bioinformatics-based concepts to catalogue information on genomic diversity, (ii) develop a data warehouse for data export/import according to international standards and protocols, (iii) provide intuitive and user-oriented interfaces for data-retrieval and comparison, (iv) define existing and upcoming BIG-DATAsets (all -omics, passport, climate, geographic origin, etc.) to be accommodated in the future, and (v) evaluate strategies and analysis pipelines for utilizing vast amounts of genomic, legacy, and passport information for detailed population genetic analyses and to support educated selection of material for pre-breeding programs. The project will generate the fundamentals to prelude a sweeping change in managing of and providing informed access to ex situ collections.
The increasing demand for experts to handle and analyze BIG Data in a scholarly and vocational context requires capacity building in the interdisciplinary field of plant breeding, genomics and bio-/diversity-informatics. Benefiting from close collaboration within the ScienceCampus Plant-based Bioeconomy of Martin-Luther-University Halle-Wittenberg we will teach and train undergraduate and graduate students to introduce them into the fundamentals of genomics of genetic resources and related topics in the field of Bioinformatics. In the same context, we will seek close interaction / collaboration to similar activities underway for other species, e.g. wheat (CIMMYT1), rice (IRRI1, Shanghai University1) and cassava (NEXTGEN Cassava1), and we will coordinate for implementing international standards with the DivSeek Initiative and the Global Plant Council1, coordinated under the umbrella of the Global Crop Diversity Trust1. This collaboration will form a nucleus to ramp up the global information system of PGR as postulated in the International Treaty (§17) .
1 expression of support and collaboration interests are available to IPK
Scientific and technological aims:
- Create a genome diversity catalogue for an entire IPK germplasm collection (Hordeum vulgare) which is of highest relevance both for research and crop improvement;
- Estimate the genetic purity at accession level, analyze patterns of molecular diversity and estimate relatedness among individual accessions;
- Identify a core collection of main representative haplotypes for in-depth re-sequencing and allele mining for major traits and characters;
- Use catalogued SNPs for association genetic analyses, exploiting historic legacy as well as newly generated phenotypic data as a foundation for trait mapping and gene discovery.
- Develop a bioinformatics infrastructure for sharing, visualizing and exploring the atlas of genetic variation;
- Develop algorithms and tools to facilitate identification of appropriate germplasm and prediction of agronomic performance and direct pre-breeding efforts;
- Deploy above mentioned infrastructure and tools to enhance IPK¿s Genebank Information System (GBIS) and the European Search Catalogue for PGR (EURISCO) to improve conservation management and utilization.
- Evolve the Federal ex-situ Genebank from a resource centre into a combined resource and information/knowledge centre for crop plant diversity;
- Develop innovative concepts for better utilization and improved collection management: identify redundancies, monitor genetic integrity during future reproduction cycles, identify gaps to be filled by future collection and/or acquisition;
- Strengthening IPK¿s Biodiversity Informatics portfolio and expertise;
- Strengthening the visibility of the Federal ex-situ Genebank by becoming a trend-setter in biodiversity/genebank data warehousing;
- Capacity building in (bio)informatics and genomics of PGR.
Scientific and economic potential:
- Unprecedented access to a genomic diversity catalog of the entire barley collection to generate new knowledge and to develop improved cultivars;
- Development of a data warehouse infrastructure, adoptable by international genebanks;
- Contributing to global policy making of managing/ utilization of crop diversity collections;
- Unlocking the potential of natural genetic diversity for a global top five crop species for pre-breeding and crop improvement;
- Initiate broad-scale gene discovery and allele mining for agronomic traits and biological characters of the crop species;
- Help choosing appropriate accessions to better meet user´s requirements and to reduce resources required to process and distribute more than 30.000 seed samples p.a.