Current and future pangenomic research in cucurbit crops

Abstract

Pangenomics is the exploration and characterization of the full spectrum of genetic variation within a species or a given taxonomic clade. Driven by the accelerating decline in sequencing costs and the widespread adoption of long-read sequencing technologies, the “wave” of pangenomics is now hitting various major crops, uncovering substantial intraspecific diversity previously underestimated and neglected. This includes crops belonging to the gourd family (Cucurbitaceae), such as cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), wax gourd (Benincasa hispida), and bottle gourd (Lagenaria siceraria), all of which are important on a global or regional scale. In this review, we consolidate the findings from all nine pangenomic studies reported as of June 2024, on the five cucurbit crops listed above. This summarizes the current state of pangenomics in the family. We then highlight remaining knowledge gaps for each crop, and propose further research to fill these gaps. Finally, we discuss how pangenomics will shape the future of crop breeding and expand the framework of crop genetic resources in synergy with other technological advances. These insights would apply not only to cucurbits but also to crops across diverse families.