Researchers from the EU-funded GAIN4CROPS project, publishing in Nature Plants, report breakthrough findings on the molecular patterns underlying C4 photosynthesis — a more efficient form of photosynthesis that reduces energy loss from photorespiration. This work provides a rich resource of single-cell expression atlases and identifies a conserved set of gene regulators across independent C4 lineages, advancing our understanding of how nature repeatedly achieves high carbon-fixation efficiency.
Photorespiration, a by-product of the key enzyme RuBisCO’s interaction with oxygen, reduces the efficiency of CO₂ assimilation and can lower plant biomass by up to ~30%. Reducing these losses is central to GAIN4CROPS, an ambitious European initiative that over five years has developed novel strategies to overcome these metabolic inefficiencies and improve yield in C3 crops like sunflower.
The Nature Plants study, lead by our partner Prof. Julian M. Hibberd from the Department of Plant Sciences at the University of Cambridge (UK), uses single-cell and single-nucleus RNA sequencing to map gene expression in leaves of two independently evolved C4 dicot species (Gynandropsis gynandra and Flaveria bidentis). This high-resolution analysis reveals that bundle sheath cells in both C4 species retain gene-expression patterns similar to mesophyll cells of C3 plants, pointing to conserved regulatory modules that have evolved repeatedly across plant lineages.
Among the key findings is the identification of transcription factors from the C2H2 and DOF families that are shared in the bundle sheath cells of both C4 species. These regulatory elements likely underpin the spatial partitioning of photosynthetic processes — a hallmark of C4 efficiency.
“Our single-cell resolution datasets deliver unprecedented insight into how plant cells organize gene networks to achieve enhanced carbon fixation,” said Tianshu Sun, Postdoctoral Research Associate and lead author of the study.
These resources will be invaluable for both basic plant science and translational efforts aimed at boosting crop productivity in a warming climate.
The release of this dataset also includes a web-accessible visualization portal, enabling researchers worldwide to explore gene expression patterns across cell types and species.
How This Supports GAIN4CROPS and Future Crop Innovation
Understanding the genetic and regulatory foundations of photosynthetic efficiency is critical for engineering C3 crops with minimized photorespiration — the core ambition of GAIN4CROPS. Over its five-year lifespan, the project has developed and validated disruptive technologies and synthetic metabolic pathways inspired by natural C3-C4 intermediates, laying the groundwork for next-generation high-yielding crop varieties.
Project coordinator Prof. Andreas Weber noted:
This publication demonstrates the power of combining cutting-edge single-cell technologies with evolutionary insights. It aligns with our mission to translate fundamental plant biology into tangible gains in crop productivity and resilience.
The full study is published as:
Sun, T., Bonthala, V. S., Stich, B., Luginbuehl, L. H., & Hibberd, J. M. (2025). Conserved spatial patterning of gene expression in independent lineages of C4 plants. New Phytologist.
