Tree Fruit and Nut Crops at the Dawn of the Pangenomic Era

Tree fruit and nut crops are a critical component of the global economy, producing at least 400 million tonnes of produce in 2022 and nourishing a growing population of approximately 8 billion humans every year. Improved cultivars and growing practices depend upon an understanding of the molecular basis of tree traits and physiology. Over the past 20 years, the proliferation of reference genomes for tree fruit and nut crop species has transformed the study of genetics in these crops, providing a platform for resequencing analyses of large populations, enabling comparative genomic analyses between distant plant species, and allowing the development of molecular markers for use in breeding. However, reference bias and poor transferability of markers limit widespread applicability in many instances. As third-generation sequencing has become more accurate and accessible, a greater number of reference genomes have become available, enabling higher-quality assemblies and wider sampling of genomic diversity. To facilitate the effective use of multiple closely related genomes to create a reference and comparative genomics platform, tools have been developed for the creation of pangenome graphs, a data structure using nodes connected by edges to represent multiple genomes and their sequence variations. Pangenome graphs allow for singular representations of diversity within a species or even a wider genus. Pangenomic analyses at the genus-scale (e.g., Malus, Citrus) have been conducted for Malus and Citrus, and more tree fruit and nut species are likely to follow. As the number of genome sequences and pangenome resources increases, the importance of generating great quantities of transcriptomic and phenomic data will increase as well. This data is essential in the drive to connect genes to traits and overcome traditional breeding bottlenecks, which is needed to develop improved tree fruit and nut crops, which can satisfy global demand.