Genotyping-by-sequencing of the European garlic collection to develop a sustainable ex situ conservation strategy
Activity Coordinator: Manuela Nagel
The Garli-CCS Activity, submitted by the Allium, Cryopreservation, and Documentation & Information Working Groups for funding under the Sixth Call of the Phase X ECPGR Activity Grant Scheme, was selected by the Executive Committee and approved in December 2022.
- Activity proposal (718,5 KB)
Summary of the Activity
Garlic is an important crop in Europe, with about 3,200 accessions maintained in European field genebanks. The ECPGR Garli-CCS Activity aimed to develop an efficient conservation strategy for European garlic accessions combining cryopreservation with measures to improve usability for breeders and producers through prioritization, rationalization and acquisition activities.
Major achievements include:
- Genotype-by-sequencing (GBS) data generated for 2,434 accessions from 16 European and one international genebank
- Phenotypic data provided for 1,731 accessions, enabling genetic analyses and supporting breeding programmes
- Training in garlic cryopreservation for 20 scientists, with four partners receiving advanced instruction to strengthen European cryopreservation capacity
- Exchange of methods and procedures through three online and one in-person meeting, enhancing collaboration among European partners.
By April 2026, two new reference genomes will be produced to fully exploit the GBS data and deepen the understanding of European garlic diversity. This knowledge will support prioritization of genotypes for cryopreservation, the establishment of a European garlic core collection with centralized access for breeders and researchers, and the development of a comprehensive long-term conservation strategy.
For more information on the project outputs, please read the Activity report
Implementation
October 2025
The final Activity Report is available here (719,9 KB)
May 2025
From 20-22 May 2025, IPK Gatersleben, Germany hosted the Garli CCS Grant Scheme Activity meeting in the context of the Gatersleben Allium Symposium. During the meeting, held back-to-back with the 9th meeting of the ECPGR Allium WG, partners discussed Garli-CCS data, as well as genebanks conservation and cryopreservation strategies.
September 2024
The Garli-CCS-Cryopreservation workshop was held on 17-20 September 2024 in Prague, Czech Republic. [Draft agenda (409,2 KB) | List of participants (206,1 KB)]
The workshop aimed to transfer the knowledge acquired by the Crop Research Institute Prague, and IPK Gatesleben cryopreservation teams to other institutions dealing with Allium cryopreservation. Three different approaches to garlic cryopreservation were introduced and trained: Cryopreservation of apical shoot tip from explants, apical shoot tip from bulbils, and of glove's basal plates. The course introduced a technique that can be applied to the specific plant material coming from in vitro or field conditions. At the end of the training school, the participants will know the necessary to apply the technique in their respective cryobanks. Furthermore, the participants are expected to apply new knowledge and skills to cryopreserve samples in garlic collections in their home institutes and their experience, results and advances will be compared.
September 2023
The second virtual Garli-CCS meeting took place on 22 September 2023 with the aim to start thinking about selection criteria for duplicate identification of garlic accessions and progress on the genotyping of the IPK collection.
March 2023
The first virtual Garli-CCS meeting took place on 10 March 2023 to introduce all project partners, clarify the distribution of the project money, describe the sampling strategy and discuss the first steps.
The video of the meeting is available [here]