Translating Stress Memory to Resilience: Current and Future Feasibility of Phenomics, Single-Cell and Spatial Multi Omics in Crop Breeding

Abstract

Climate change has a large impact on crop growth and global food security because crops are under constant stress from abiotic (e.g., drought, heavy metals, extreme temperatures) and biotic (pathogen attacks) stresses. These stressors can significantly impact plant growth and productivity. By linking these changes in genes (genotypes) and or other cellular traits to phenotypes that occur under stress, researchers can better understand how plants adapt to challenging environments and pass this information on to their offspring, which is also known as plant stress memory. The mechanism by which plants remember past stressors and pass on these adaptive traits mainly consists of epigenetic changes. Learning from the mechanism of stress memories can be used for breeding crops with enhanced resilience to future environmental threats. By combining multiple -omics layers, so-called multi-omics, a perspective can be provided in understanding the molecular mechanisms underlying trait variation in crops. These layers, which include genomics, epigenomics, transcriptomics, metabolomics, proteomics, and more, provide multifactorial insights on several levels of biological regulation in crops and other organisms, thus offering crucial insights into genetic understanding and environmental adaptation for the development of resilient crops. This article reviews the current use of bulk-, single-, and spatial-multi-omics and the possibilities of the future use of spatial- and single-cell multi-omics, or a combination, to enable a more complete link between genotype to phenotype for stress memory in crops within the next two years. Although single-cell multi-omics and phenomics are considered achievable due to existing computational power and accessible technology. Spatial multi-omics remain highly challenging and unlikely to be standardized for crop stress memory research within the next two years, due to technical issues and high costs. This article review emphasizes the importance of integrating various types of multi-omics data, including genomics, epigenomics, transcriptomics, metabolomics, and proteomics, to gain a comprehensive understanding of stress memory and ultimately enhance crop breeding.