Use of multiple 'omics techniques to accelerate the breeding of abiotic stress tolerant crops

Crop production can be severely limited by adverse environmental conditions such as drought, extreme heat, and frost. As climate change intensifies, weather patterns are becoming less predictable and extreme weather events more likely. To ensure continued production of enough food for the growing world population, crop losses due to adverse conditions must be curtailed. One way to do this is to improve the level of abiotic stress tolerance in crops through breeding. The process of breeding plants has seen recent increases in speed and efficiency due in large part to the application of genome sequencing and development of high-density genetic marker panels. Using genotypic data produced by these technologies, a statistical technique known as 'genomic prediction' can predict the level of tolerance to different abiotic stresses in an individual plant. Furthermore, the development of genome editing will allow for targeted modification of specific nucleotides, to enhance abiotic stress resilience. The continued sequencing and analysis of thousands of genomes of individuals in each plant species, known as 'pan-genomics', will allow us to identify the precise polymorphisms that underlie abiotic stress tolerance. Such polymorphisms have the potential to significantly increase the accuracy of genome-assisted breeding methods, and support the identification of targets for genome editing, further enhancing the development of abiotic stress tolerant crops. In addition, use of multiple 'omics data will allow for accurate representations of the genetic pathways in crop plants that control abiotic stress responses. Coupling this knowledge with pan-genomics could further enhance the accuracy of genome-assisted breeding, increasing the efficiency of crop breeding and generating new prospects for developing abiotic stress tolerance via genome editing. In this review, we summarise recent research using 'omics techniques to understand the genetic basis of abiotic stress tolerance in plants with a focus on major food crops. We evaluate the potential avenues for improving crop production using 'omics techniques and discuss areas for future research that we think should be prioritised.