Gene Editing in Solanaceous Crops for Resistance Against Potyviruses
Background
The current geopolitical landscape and the impact of climate change underscore the need for innovative solutions in food security and sustainable agriculture. New Genomic Techniques (NGTs), particularly CRISPR-Cas technology, have emerged as powerful tools to address these challenges.
Tomatoes are the most widely produced vegetable crop in the European Union by volume, with major production in countries such as Italy, Spain, and France. Although tomato production in Estonia is limited, the crop holds significant cultural and practical value in home gardening. Notably, tomato seeds are often imported from non-EU countries, which poses a potential phytosanitary risk due to the introduction of plant diseases—also viral infections.
Potato virus Y (PVY) is the most prevalent potyvirus naturally infecting tomato plants. The molecular mechanisms of PVY infection in solanaceous crops have been extensively studied. A key factor in PVY pathogenicity is the interaction between the viral protein genome-linked (VPg) and the host plant’s eukaryotic translation initiation factor 4E (eIF4E). Disrupting this interaction is essential for developing PVY-resistant plants. In tomato, the eIF4E gene family consists of four members: eIF4E1, eIF4E2, eIF(iso)4E, and nCBP. Additionally, multiple PVY isolates exist, further complicating resistance strategies.
Some plant species possess natural resistance to potyviruses due to mutations in eIF4E genes. Where such natural mutations are absent, gene editing technologies can be employed to mimic them. Further research is required to develop targeted editing strategies that account for the diversity of eIF4E genes in different plant species.
CRISPR/Cas technology is currently the most straightforward method for inducing mutations in eIF4E genes that prevent VPg binding, thereby conferring resistance to PVY.
Main Goals
- Develop PVY-resistant Estonian tomato cultivars using CRISPR/Cas gene editing, while preserving the key agronomic traits of the original varieties.
- Advance the understanding of the molecular mechanisms underlying PVY infection in tomato.
These goals are interconnected and mutually reinforcing, providing the PhD candidate with a comprehensive foundation in applied plant biotechnology grounded in fundamental molecular research.
Key Methods
- Application of various CRISPR-Cas systems—including Base Editing and Prime Editing—on different Estonian tomato cultivars.
- Testing of guide RNAs (gRNAs) via transient expression systems, such as Nicotiana benthamiana and tomato protoplasts.
- Generation of edited plants through Agrobacterium-mediated transformation of explants or delivery of RNP complexes into protoplasts.
Perspective
The PhD candidate will be embedded within active research consortia in Estonia and France, linked to the expertise and collaborations of their supervisors. The Centre of Estonian Rural Research and Knowledge—Dr. Sarmiento’s partner—will provide Estonian tomato cultivars of regional importance. International mobility, including research stays and joint experiments with Dr. Gallois in France, will broaden the candidate’s perspective.
The position offers a unique opportunity to contribute to real-world agricultural challenges while developing advanced skills in molecular biology, plant biotechnology, and applied genome editing—positioning the candidate for a career at the intersection of basic research and practical innovation.
Dr. Cecilia Sarmiento (ORCID ID: 0000-0002-8011-1370), senior researcher, obtained her PhD in Natural Sciences (Gene Technology) from TalTech in 2008, following MSc studies at La Molina National University of Agriculture in Lima, Peru. Her research experience spans over 25 years, focusing on plant virology, RNA silencing, gene editing, and plant stress responses. Since 2009, she has been active in higher education teaching and has supervised more than ten MSc students, four PhD students and one postdoctoral researcher. In 2019, she was appointed Programme Director for Doctoral Studies at the School of Science and began leading the Plant–Pathogen Interactions and Plant Genetics research group. She has been responsible for several research projects, including the EEA-funded international project EditGrass4Food (2021–2024) and Modern Breeding Tools for Smart Food Security (2024–2027), funded by the Ministry of Regional Affairs and Agriculture. Dr. Sarmiento has authored 23 scientific publications, primarily in Q1 journals, and holds an h-index of 14 (Google Scholar). In recent years, she has expanded collaboration with European scientific institutions and the public sector. She serves on the board of the European Plant Science Organisation (EPSO) and participates in national expert groups addressing New Genomic Techniques (NGT) and GMO regulation.
Current research focus: plant molecular biology, gene editing, biotechnology, virology, stress.
Number of Publications: 23
Key Funding: EEA/Norway (2021-2023), Ministry of Regional Affairs and Agriculture (2024-2027), Infrastructure grant-ETAG (2025-2029).
Awards, memberships: State Research Prize in agricultural sciences (2009), EPSO board, ICTV (Solemoviridae Study Group)
Dr. Jean-Luc Gallois (ORCID ID: 0000-0003-0451-1740) is a plant geneticist and virologist at the Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) in Avignon, France. He obtained his PhD at Université Joseph Fourier (Grenoble, France) in 2000, followed by postdoctoral research at John Innes Centre (Norwich, UK). His main research focus is to develop genetic resistance to potyviruses in tomato, using both natural diversity and genome editing. Today, he is recognized in Europe in the field of plant genome editing, particularly in CRISPR-mediated base and prime editing. He holds an HDR (Habilitation à Diriger des Recherches), a French academic qualification that allows the supervision of PhD students. He has supervised seven doctoral candidates over the past 12 years. He has published more than 40 scientific articles. Dr. Gallois is currently involved in two flagship projects that aims at developing genome editing tools for selection as part of a national project funded by France/ANR. He also participates in the EU-funded GeneBEcon project under the Horizon Europe research and innovation programme. Since 2024, he has been hired by EFSA as an expert on the GMO panel.
Dr. Triin Vahisalu (ORCID ID: 0000-0001-6050-0320) has supervised three MSc students during the last 7 years. She is currently the main supervisor for one PhD and one Master student.
The candidate should possess a strong background in molecular biology, along with basic knowledge of plant biology and virology. Prior experience with CRISPR/Cas9 systems and plant tissue culture techniques will be considered an advantage. Proficiency in standard molecular biology techniques—such as cloning, DNA/RNA isolation, PCR, and genomic sequence analysis—is essential, as is proven hands-on laboratory experience. While prior work with plants is beneficial, it is not mandatory; however, experience working under sterile conditions is required.
The candidate is expected to demonstrate a willingness to learn and apply advanced techniques, as well as the ability to critically read and analyse scientific literature in the field. Independent and innovative thinking, combined with strong analytical and problem-solving abilities, are crucial. Effective communication skills, both oral and written, are also essential. A collaborative mindset and readiness to work as part of a team, both in Estonia and in France, are expected.