Unlocking genetic diversity in Colombian cassava landraces for accelerated breeding

Cassava (Manihot esculenta) is a staple crop across the global south, yet modern varieties may have limited genetic diversity due to historical bottlenecks. We investigated the genomic diversity of over 1000 cassava genotypes, incorporating 387 newly sequenced Colombian landraces originating from diverse climates. We hypothesized that landraces retain untapped variation useful for breeding and adaptation. Whole-genome sequencing was used to characterize landraces and breeding lines. We assessed genetic differentiation across geography and climate and analyzed the distribution of loss-of-function (LoF) mutations to identify potential targets for gene editing. Landraces maintained high and novel dimensions of genetic diversity compared to breeding lines from Asia and Africa. Differentiation among landraces reflected both demography and climate of origin. LoF analyses indicated purging of deleterious alleles through inbreeding, but LoF alleles were retained in genes enriched for coumarin biosynthesis and plant immunity, suggesting selection for postharvest quality and disease resistance. Climate-associated loci were explored for their adaptive potential. Cassava landraces represent a critical reservoir of genetic diversity. This study establishes a foundation for leveraging landrace variation to accelerate cassava improvement through gene editing and targeted breeding.