24BBR for Provision of FAIR wheat, pea, and brassica TILLING biological and functional genomics resources

To feed the growing global population while minimising the negative effect of agriculture on the environment, staple crops must yield more calories and nutrients per unit of land and energy. The raw material of crop improvement through breeding is the genetic diversity stored as seed collections in genebanks. Broadening crop genetic diversity by inducing mutagenesis has been instrumental since the 1930s, evidenced by > 3,300 FAO-listed improved varieties of 220 species deployed in > 70 countries that contain beneficial induced mutations. Coupling crop-induced diversity with genome sequencing proved highly valuable for functional genomics applications in crop science and related pre-breeding applications through reverse genetics to elucidate and validate gene function. This is evident by the high demand for the JIC Germplasm Resources Unit FAIR provision of the wheat TILLING collection. The populations’ genomes are visualised on EnsemblPlant where users can browse for a mutation in their gene of interest, obtain information regarding its potential nature and order the corresponding seed packet. Appropriate training materials are accessible to ease the use of this public resource; they were explicitly designed to target model-plant researchers supporting the deployment of their expertise directly on wheat crops and wheat breeders with no strong bioinformatic support teams. As a result, 14,348 seed packets have been sent from the GRU since 2015, when the wheat TILLING population central provision started, following the completion of a dedicated BBSRC BBR funded project (BB/I000712/1). The seeds were sent in response to 755 users’ requests, of which 61.5% were UK-based. A total of 2,272 freedom-to-operate commercial licences were signed with breeding companies. These populations are sustainably conserved as users recover the annual costs of seed stock replenishment and quality tests. Recent developments in high throughput phenomics and bioinformatics have opened new avenues for using the genome-sequenced induced genetic diversity populations in a forward genetic manner where no specific gene is targeted. Instead, entire populations are evaluated for an advantageous trait (e.g., disease resistance), and the effect of sequenced mutations on the trait is studied on a whole genome scale. This trend for accelerated gene discovery is shifting the demand toward larger germplasm subsets. Following in the impactful footsteps of the wheat TILLING resource, we propose to provide the UK bioscience community with three additional FAIR TILLING resources of mutated seed populations coupled with bioinformatically-digested, user-friendly genomic information: gamma radiation-induced deletion mutation in wheat; fast-neutron-induced deletion mutation in peas; chemically-induced point mutations in Brassica rapa. This work is timely because the three resources were recently genome-sequenced and annotated (yet unpublished). In addition, high-resolution reference genomes of the three genetic backgrounds are available for our work (yet unpublished). Adhering to the cherished FAIR principles, we will develop the genomic visualisation framework needed to reap a maximal value from the mutated germplasm available from SeedStor (https://www.seedstor.ac.uk/), display the novel genomic data on EnsemblPlants (https://plants.ensembl.org/index.html), develop sector targeted training materials, enhance the deposited seed quantity, quality and future proof them to initiate their sustainable community use. By doing so, we will develop synergistic pathways to ease the deployment of future-induced diversity crop resources to benefit UK crop science and pre-breeding communities in supporting global food security.