Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abstract Wheat is a crucial crop globally, with widespread cultivation and significant economic importance. To ensure food security amidst the increasing human population and new production challenges, such as climate change, it is imperative to develop novel wheat varieties that exhibit better quality, higher yield, and enhanced resistance to biotic and abiotic stress. To achieve this, leveraging comprehensive genomic resources from global breeding programs can aid in identifying within-species allelic diversity and selecting optimal allele combinations for superior cultivars. While previous single-reference genome assemblies have facilitated gene discovery and whole-genome level genotype–phenotype relationship modeling, recent research on variations within the pan-genome of all individuals in a plant species underscores their significance for crop breeding. We summarize the different approaches and techniques used for sequencing the large and intricate wheat genome, while highlighting the challenge of generating high-quality reference assemblies. We discuss the computational methods for building the pan-genome and research efforts that are aimed at utilizing the wheat pan-genome in wheat breeding programs.