Dissecting epistasis for enhanced crop productivity

Project Information

EPICROP

Grant agreement ID: 802008

DOI

10.3030/802008

Project closed

EC signature date 14 January 2019

Start date 1 August 2019

End date 31 July 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 903,00

EU contribution

€ 1 499 903,00

Coordinated by

UNIVERSITE DE LAUSANNE
Switzerland

Periodic Reporting for period 4 - EPICROP (Dissecting epistasis for enhanced crop productivity)

Reporting period: 2024-02-01 to 2025-07-31

Summary of the context and overall objectives of the project

A frontier in genetics is to understand how complex genotypes translate into quantitative trait variation. In breeding, gene mutations can have beneficial effects in one genotype but cause detrimental outcomes when introduced into a distinct genotype, which is due to interactions with mutations in the new genotypic context. Such genetic interactions are also known as epistasis and represent a hurdle for targeted trait breeding in plants and animals because they complicate the prediction of breeding outcomes when combining gene mutations. In this project, my team aimed at better understanding the molecular principles of genetic interactions in crops and at revealing hidden mutations that arose during domestication and modulate flowering traits in the model crop tomato. For this, we investigated the interaction between genes that regulate the activity of plant stem cells, which give rise to above-ground organs and eventually flowers and fruits. In a first aim, we focussed on a group of regulatory genes to study how genetic interactions affect the dynamics of gene expression during stem cell development. We discovered that genetic interactions emerge from duplicated genes that partitioned functions to regulate inflorescence architecture and floral organ identity. Moreover, extensive phenotypic changes from genetic interactions are reflected in only few genes with synergistic transcriptional changes that coordinate expression programs across successive developmental windows. In a second aim, we applied genome editing to uncover how mutations are modified in diverse tomato varieties and revealed genes that changed during domestication and breeding for adaptations in flowering. Notably, we applied base editing to directly repair a deleterious variant in domesticated tomato to generate plants with compact growth and early fruit yield. Furthermore, we fine-tuned inflorescence architecture and flower production by engineering genetic interactions using multiplex genome editing. Our findings in tomato suggest that genetic background effects are widespread among flowering traits and that genetic interactions can be engineered by genome editing for predictable trait improvement. The outcome of this project advances our understanding of genetic interactions in crops and outlines novel strategies for predictable trait breeding for bringing more resilience and sustainability into agricultural production systems.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the course of this action, we developed a new toolset for automated assembly scaffolding and generated chromosome-level assemblies for a novel fast-cycling genotype called S100 that we established as system for high-throughput genome editing (Alonge et al., Genome Biol, 2022). We expect that this novel genotype, which nearly doubles the number of generations per year, will become the foundation for genome-wide editing experiments in tomato. Finally, our approach outlines strategies for rapidly generating diverse personalized reference systems in other species. Since genome editing experiments in tomato are still limited by laborious protocols to regenerate stably transformed plants that express editing reagents, we set out to enhance plant regeneration. We constructed a tomato morphogenic regulator chimera (SlGRF-GIF), which reliably improves of regeneration efficiency by nearly two-fold, while also shortening the time to obtain transgenic plants by approximately one month (Swinnen, Lizé et al., Plant Biotech J, 2025). We utilized this new system for CRISPR-Cas experiments to target meristem regulator genes in tomato, showing a simplified isolation of desired genome edits in both single and multiplex targeting approaches. We investigated how crop domestication led to potenitally harmful mutations that are deleterious for gene activity by computing the accumulation of deleterious mutations during tomato domestication (Glaus et al., Nat Genet, 2025). We identified a deleterious variant that disrupts the DNA-binding domain of a transcription factor and floral regulator. The loss of transcription factor activity broke functional redundancy with a closely related gene and allowed the utilization of a mutation to optimize tomato productivity. Finally, we used base editing to directly repair the deleterious mutation in domesticated tomato and obtained compact plants with early fruit yield. These findings illustrate how deleterious variants can become adaptive due to interactions with mutations that are introduced during breeding, which has an impact on genome editing in agriculture.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Pan genomes capture the genetic diversity within and between species at unprecedented accuracy. Yet, to functionally interrogate this vast genetic variation we need a transition from single references to many diverse experimental systems. Such custom references will be enabled by personalized genomes that allow precise genetic dissection at scale. However, the major bottleneck for establishing collections of personalized genomes is the laborious process of assembly scaffolding. To overcome this limitation, we develop a new tool to automate genome assembly scaffolding and applied this tool to different tomato genotypes, including a novel fast-cycling genotype that presents a significant advantage for genetics experiments due to its short generation time and space requirements. We expect that this genotype and the new genomic resources will be widely adopted by the community for future genome editing experiments at scale.

The intense artificial selection during domestication shaped plant and animal genomes to adapt their traits to human preferences. However, domestication also led to an accumulation of potentially harmful mutation that are deleterious for gene activity, a process often referred to as “the cost of domestication”. With recent advances in genome editing it has been proposed to use precision editing tools to directly repair deleterious variants and reduce the mutational load of domesticated genomes. Yet, up to our study, an experimental demonstration was lacking. We use base editing to directly repair the deleterious variant in domesticated tomato and obtain plants with compact growth and earliness for fruit yield. This application of base editing represents the first time that precision genome editing is applied to directly repair deleterious mutations in crops. However, our findings also illustrate how deleterious variants can become adaptive in domestic environments due to genetic interactions with mutations that are introduced or arose during breeding, which has an impact on genome editing strategies that are applied in agriculture.

Engineering genetic interactions by genome editing for predictable trait improvement