Research

Engineering Synthetic Plant Chromosomes (synPACs)

Advances in synthetic genomics have opened new pathways for engineering biology, enabling the rapid design and construction of biological systems at scale for innovative applications and to address fundamental scientific questions.

Summary

Project Summary.

Funded by:

Advanced Research + Invention Agency (ARIA)

Synthetic Plants Programme

Conventional breeding has been essential for ensuring food security and improving crop traits over centuries. However, traditional plant breeding and selection can take decades to introduce beneficial traits, relying on random genetic mixing over multiple generations.

Modern agriculture is facing significant challenges, from climate instability, soil degradation, changes in land use, and conflicts drastically impacting global food security. This requires us to rethink how we develop new crops to feed our growing populations, replace fossil fuels, and provide new platforms for biomanufacturing.

Funded by a multimillion pound grant from the UK Government’s Advanced Research + Invention Agency (ARIA) as part of the Synthetic Plants programme, a multidisciplinary collaboration of researchers from Earlham Institute, University of Manchester, and John Innes Centre is leveraging these advances to establish synthetic plant chromosome (synPAC) technologies.

The research team aims to develop critically needed synthetic chromosome technologies with a robust and reproducible engineering system to allow the targeted programming of plants at a scale that can transform food security.

Building on natural processes, synPACs enable researchers to rapidly introduce multi-gene traits in a far more precise, controllable, and predictable fashion — offering an innovative alternative to conventional breeding methods.

Detail

Details.

The first phase of the project will focus on potatoes, a globally important crop, with the goal of developing technology pipelines to fast-track plant engineering.

Initial target traits will include enhanced nutritional content and resilience against environmental stressors, as well as improving agricultural sustainability by reducing reliance on chemical inputs.

By enabling plants to efficiently produce valuable compounds, synPACs could also support the development of new, plant-based sources of essential nutrients and bioactive compounds, potentially benefiting both human health and the environment.

The study builds on a long-term collaboration with an international consortium of scientists led by Prof Patrick Cai at University of Manchester to generate the first fully synthetic yeast genome.

The research consists of three main components:

Aim 1 establishes the design infrastructure, including powerful genome software tools for design, manufacturing, and testing.
Aim 2 focuses on construction, with the rapid assembly of million-base-scale DNA constructs in yeast, followed by the synthesis of the components that will form complete synPACs.
Aim 3 addresses challenges in delivery from yeast to plant cells, including secondary strategies of constructing synPACs in planta.

The Earlham Institute will lead on three areas of the project.

Professor Anthony Hall will oversee the development of a potato tissue atlas and characterisation of regulatory elements. To achieve this, we will harvest existing published potato gene expression data together with our existing RNAseq datasets, then use machine learning approaches to identify regulatory regions.
The assembly and testing of a potato regulatory element library will be led by Dr Carolina Grandellis through the Earlham Biofoundry, using automated high-throughput DNA assembly workflows and protoplasts testing.
While Dr Conrad Nieduszynski’s team leads on engineering synthetic chromosome stability in yeast and plant cells.

Collaborators

Impact statement.

synPAC technologies have the power to remove breeding bottlenecks and provide powerful new ways of introducing novel traits to plants —such as producing essential nutrients or increased pest resistance—while maintaining the plant’s existing characteristics.

Synthetic bacterial and yeast projects have shown the feasibility of constructing entire synthetic genomes, yielding promising results for both research and industry.

Applying these breakthroughs to plants is the next logical step, filling a longstanding gap in agricultural innovation by unlocking engineering biology in plants at a previously inaccessible speed and scale.