Genotyping-by-sequencing of the European garlic collection to develop a sustainable ex situ conservation strategy (GarliCSS)

Project aim: The aim of the activity is to develop an efficient conservation strategy for European garlic accessions in conjunction with the implementation of cryopreservation and increased usability of garlic accessions for breeders and producers through prioritization, rationalization and acquisition activities.

Project activities:
To develop the strategy, the work is conducted with five work packages:
1.    Sequencing 
WP 1.1 Partners will collect leave material from young single plants in AprilMay – June 2023, dry over silica gel and post to Partner 1. 
WP 1.2 Partner 1 (M. Nagel, F. Blattner and D. Harpke) will extract DNA, submit DNA to sequencing (F. Blattner and D. Harpke). After the marker information will be generated, the data will be stored in existing database structures of the IPK and can be made immediately available to material providers on request.
WP 1.3 Partner 1 (F. Blattner and D. Harpke) will analyze marker data and provide results for discussions.
2.    Phenotyping (April – September 2023 and 2024)
WP 2.1. To increase the attractiveness of the accessions and the breeding value of the material, garlic accessions used for sequencing will be phenotyped by all partners for the traits; a) Ability to produce scape (7.2.1), b) Bulb structure type (7.1.20) and c) Shape of mature bulb (7.1.12). The phenotyping data will be compiled and the respective National Inventory Focal Points will be approached to submit the data to EURISCO. 
WP 2.2. The combination of phenotyping and sequencing data will also enable a genome-wide association (GWAS) analysis, conducted by Partner 1 (M. Nagel), and identify marker-trait association and loci responsible for bulb weight and size. This information will stimulate further breeding processes and support activities such as marker-assisted selection. The results of the GWAS will be made available via an open access publication. 

3.    Data accessibility (December 2023 and 2024)
WP 3.1 After evaluation and verification, Partner 1 (S. Weise) will upload the data to the EMBL-EVA public repository. 
WP 3.2 Subsequently, links will be established in EURISCO between the corresponding accessions documented there and the genotyping data.

4.    Cryopreservation training (October - December 2024)
WP 4.1 Partner representing the CRYOPRESERVATION group will organize for the consortium members, a cryopreservation workshop in Prague. Overall, 7 participants and 2 experts from abroad will be invited to discuss procedures, provide guidance and training on garlic cryopreservation. 
WP 4.2. All partners implementing cryopreservation will be involved to develop cryopreservation strategy which includes thresholds for the number of shoot tips for safety duplicates, number of replicates, locations for safety duplications and additional support by online trainings and meetings. The cryopreservation strategy should be considered a model for clonal plants. Therefore, a two-day virtual meeting is planned. The first day of the meeting will summarize the experiences of the workshop organizers and participants. The second day will be devoted to a discussion of the cryopreservation strategy. The number of participants will not be limited. This meeting will take place in late 2024 or early 2025 (before the last WP5 meeting).

5.    Garlic conservation strategy (Whole project period)
WP 5. All partners will discuss a conservation strategy in four online meetings taking place in the 1., 6-7th., 12-14th and 18-20th project months and one final face-to-face meeting at IPK in 22-24th months . GBS data available from IPK collection will be used as preliminary dataset for discussion of the following topics 

• Determinants and thresholds for unique accessions 
• Determinants and thresholds for duplicate accessions 
• Prioritization of garlic accessions for cryopreservation
• Prioritization of garlic accessions for a European Core Collection
• Gap analysis and acquisition strategy

The project results will be published until December 31, 2025.