Tomato and its relatives are breaking the genomics barriers

Recent advances in high-quality genome sequencing have revolutionized research in the tomato clade (Solanum section Lycopersicon), enabling the generation of long-read and even chromosome-scale assemblies for cultivated tomato and its wild relatives. These data have shed light on tomato domestication and population genetics and have facilitated breeding using exotic germplasm. This review summarizes progress in tomato genomics, focusing on the diversity of section Lycopersicon and its function as a reservoir of stress-tolerance genes, including drought tolerance from Solanum pennellii and pathogen resistance from Solanum habrochaites and Solanum chilense. We catalog important genetic resources, including introgression lines and multi-parent advanced generation inter-cross (MAGIC) populations, which have allowed the dissection of important traits via the mapping of quantitative trait loci, including those involved in primary and secondary metabolism. We also explore the metabolic diversity of wild and domesticated tomato species and discuss how this has led to gene identification. Finally, we show that tomato genomics will continue to accelerate, given the increasing availability and accessibility of genomics technology, exotic germplasm, and mapping populations, which can be leveraged using advanced genome-editing approaches.