Case study
Assessing the genetic diversity of the shamrock, Trifolium dubium, across Ireland
In 2023, a high-quality reference genome for Trifolium dubium, widely recognized as the shamrock, was generated as part of the ERGA Pilot Project. Researchers at University College Dublin (UCD) have been using this genome to study its evolutionary history and beneficial traits, which could enhance breeding programs for agriculturally important clover species.
Assessing the genetic diversity of the shamrock, Trifolium dubium, across Ireland
Katie Herron is a PhD student at UCD, focusing on the genomics of Trifolium dubium and is a member of ERGA.
Ann Mc Cartney is an Assistant Researcher in the Genomics Institute at University of California, Santa Cruz and an Adjunct Assistant Professor at UCD. She is also vice-chair of ERGA and is a member of the Executive Board of the EBP.
Graham Hughes is an assistant professor at UCD, and the director of the UCD Centre for Bioinformatics. He also sits on the ERGA Council of Representatives as representative for Ireland.
In 2023, a high-quality reference genome for the clover Trifolium dubium was generated as part of the ERGA Pilot Project. This was significant not only for its scientific value but also for its cultural importance, as T. dubium, or the lesser trefoil, is broadly accepted as being the shamrock – a well-loved national symbol of Ireland. At University College Dublin (UCD) we have been using this genome to investigate the evolutionary history of this culturally important species and to place it in the broader evolutionary context of the Trifolium genus. Trifolium includes a number of agriculturally significant species, namely white clover (T. repens) and red clover (T. pratense), which are commonly used as forage crops due to their high-protein content and nitrogen-fixing capabilities, both reducing the need for synthetic fertilisers and improving soil health. T. dubium is noted for its production of condensed tannins, that reduce bloat in dairy cattle, and its frost tolerance, potentially offering benefits over white and red clover during the Irish winter. Understanding the genetics underlying these beneficial traits in T. dubium has applications in informing breeding programs to improve other clover cultivars.
T. dubium, with its distinctive yellow flower and trifoliate leaves, mythologised to have been used by St. Patrick to explain the Holy Trinity. Photos by: Katie Herron.
TRIDUBIRE is Ireland’s first population genomics study of the lesser trefoil, Trifolium dubium – known to many as the shamroc. Project website: https://tridubire.github.io/
This study has now expanded to include a population genomics study of T. dubium, as part of BGE’s “Enhancing Biodiversity Genomics Applications” program. We plan on using pooled sequencing (pool-seq) to assess the genetic variation within and between populations of T. dubium across Ireland, sampling from both mainland Ireland as well as outlying islands. We aim to explore the species’ adaptive potential, gene flow and demographic history. By providing a genetic baseline for T. dubium in Ireland, the project will support the tracking of changes in genetic diversity over time, the identification of potential threats from environmental changes, and ultimately guide conservation strategies to preserve this culturally significant species. A key component of our project is our outreach and educational efforts through which we hope to elevate the profile of biodiversity genomics in Ireland. By involving schools, we aim to engage students in real scientific research, promoting STEM education and fostering a deeper appreciation for biodiversity at local level.
Field sampling of T. dubium across Ireland. Photos by Katie Herron and Graham Hughes.
This project will not only provide valuable data for the scientific community but also contribute to the broader goals of BGE-ERGA by underscoring the importance of high-quality reference genomes in supporting the conservation of European biodiversity. Additionally, this study can serve as a model for other widespread species in Ireland, demonstrating the utility of the application of genomic methods in conservation and agriculture. This project has received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government.
Header image: T. dubium, with its distinctive yellow flower and trifoliate leaves, mythologised to have been used by St. Patrick to explain the Holy Trinity. Photo by: Katie Herron
