3Dwheat, A 3 Dimensional functional genomics approach to identify hidden targets controlling heat stress and priming in wheat

Project Information

3Dwheat

Grant agreement ID: 101044399

DOI

10.3030/101044399

EC signature date 23 June 2022

Start date 1 September 2022

End date 31 August 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 999 995,00

EU contribution

€ 1 999 995,00

Coordinated by

UNIVERSITE PARIS CITE
France

Periodic Reporting for period 1 - 3Dwheat (3Dwheat, A 3 Dimensional functional genomics approach to identify hidden targets controlling heat stress and priming in wheat)

Reporting period: 2022-09-01 to 2025-02-28

Summary of the context and overall objectives of the project

Global food security is increasingly under threat due to the dual pressures of climate change and rising demand. With the global population expected to reach 9.2 billion by 2050, experts estimate that food production will need to double to meet future needs. Historically, advances in traditional breeding techniques, mechanization, and irrigation have driven significant yield increases for major crops. However, climate change, particularly global warming, now poses a significant obstacle to further progress. The Intergovernmental Panel on Climate Change (IPCC) highlighted crop heat stress as a critical risk to global food supply in its fourth assessment report. Wheat, the third most-produced cereal and the top crop in global trade, has often struggled to meet market demand, a challenge expected to intensify as demand rises by 60% by 2050. Heat stress is a significant limitation to wheat productivity, necessitating innovative solutions. Addressing this issue requires a deeper understanding of the molecular mechanisms governing heat stress and the development of tools to produce heat-tolerant varieties of bread wheat (Triticum aestivum). Over recent decades, wheat breeding has benefited from identifying favorable genetic variations, driven by advances such as sequencing the wheat genome, studying related species, and employing Quantitative Trait Loci (QTL) mapping and Genome-Wide Association Studies (GWAS). In the post-genomic era, exploring regulatory networks that control heat stress has emerged as a promising strategy. Epigenetic mechanisms, including histone modifications and DNA methylation—both reversible processes—play a crucial role in helping plants adapt to environmental challenges. While significant progress has been made in understanding these processes in model plants like Arabidopsis thaliana, applying this knowledge to crops with larger and more complex genomes, such as wheat, remains a relatively underexplored frontier. The 3Dwheat project seeks to advance our understanding of how epigenetic regulation influences heat stress resilience in wheat. By integrating multiple layers of regulation, rather than focusing solely on specific epigenetic markers, the project aims to develop a comprehensive toolkit. This approach holds potential not only for fundamental research but also for addressing practical challenges in wheat breeding, ultimately enhancing crop productivity in the face of a changing climate.

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

NGS technologies have revolutionized genomic research, shifting the focus from gene-specific studies to genome-wide analyses. This paradigm shift has made it feasible to apply such approaches to plants with large genomes, like wheat. NGS provides powerful tools to explore the epigenome and transcriptome comprehensively. However, recent research suggests that understanding global chromatin architecture—such as loops, domains, and territories within the nucleus—is essential for deciphering gene expression regulation. This 3D organization enables interactions between promoters and distant regulatory elements, often involving non-coding RNAs, adding a structural dimension to genomic regulation. Advances in techniques for mapping chromatin architecture have revealed its regulatory significance in plants, such as its role in developmental processes and environmental responses. For instance, studies have described nuclear architectures in species like Arabidopsis, rice, maize, and cotton, and proposed that environmental factors like cold stress can globally de-condense the genome in rice. Despite these insights, the molecular connections between chromatin structure and gene expression remain largely unexplored. In our project we addressed this knowledge gap by examining the transcriptome, epigenome, and 3D chromatin structure of wheat under heat stress.

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)

This integrative approach allowed us to uncover how chromatin-level changes influence gene expression in a polyploid plant, providing a global perspective on stress adaptation mechanisms.