Trilateral FPP 2023 - Homoeolog-aware gene networks at single-cell resolution to improve cold tolerance in wheat

• Applicant: Professorin Dr. Andrea Bräutigam
• Subject Area: Plant Breeding and Plant Pathology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 553112911

The changing and unpredictable weather patterns caused by climate change are having major effects on the yields of staple crops. Many staple crops are polyploid, including wheat, oats, bananas and potatoes, meaning that their DNA has been duplicated and they have multiple copies of each gene in each cell. Having multiple copies of each gene can give polyploid plants more options for gene function due to different combinations of gene expression; this complex orchestration may improve mechanisms for plant resilience and adaptation. Multiple gene copies can also result in genetic redundancy which can slow breeding progress. In this project we focus on cold tolerance in wheat which addresses a major breeding challenge, and serves as a case-study to develop methods which can be applied to other polyploid crops and stress conditions. Climate change is altering weather patterns, increasing the severity of winter cold in key wheat growing regions including Europe, North America and China. These unpredictable cold events can cause up to 50% yield losses. Breeding for cold tolerant wheat varieties to combat these events is a challenge: phenotypic screening in breeding populations relies upon predictable cold events at trial sites, yet climate change has reduced the number of sites that reliably receive sufficient frost events. There is an urgent need to identify new routes to enhance cold tolerance in winter wheat to provide reliable wheat production. We will use a novel approach to unlock the potential in the polyploid wheat genome to enhance cold tolerance. The aims of this project are 1) to identify novel genetic loci influencing cold tolerance in wheat and 2) build a framework to investigate stress responses in polyploid crops which allows us to exploit hidden genetic variation for crop improvement. To achieve these aims we will leverage high-resolution single-cell genomics to understand cold responses within individual cells and the responses of individual gene copies. This data will allow us to build network models to predict gene expression in cold tolerance, with a particular focus on the relevant cis-regulatory regions of genes for breeding targets. In collaboration with RAGT Seeds, a leading European wheat breeding company, we will complement our high-resolution genomic analysis with genetic studies on diverse wheat lines under controlled environments and field conditions to prioritize candidate regions for experimental testing that are most likely to have real-world benefits. We will test novel genes/chromatin regions’ effects on cold tolerance using gene editing and biparental mapping populations. This project will detect novel genetic variants that regulate cold tolerance in wheat which can be rapidly adopted in wheat breeding programs, and build a framework to unravel the complex genomic responses to stress in polyploid crops. Our approach will be broadly applicable to polyploid crops and contribute to climate resilient crop breeding.

• DFG Programme: Research Grants
• International Connection: United Kingdom, USA
• Partner Organisation: Biotechnology und Biological Sciences Research Council (BBSRC); United States Department of Agriculture (USDA); National Institute of Food and Agriculture (NIFA)
• Cooperation Partners: Philippa Borill, Ph.D.; Professor Robert J. Schmitz, Ph.D.