Exploring genetic diversity and selective signatures, a journey through Colombian cassava's landscape

Cassava (Manihot esculenta Crantz) is a prioritized crop for food security for nearly one billion people worldwide. We examined the genetic structure and diversity in a panel of 176 cassava cultivars from diverse biogeographic regions of Colombia using a total of 57,410 SNP markers obtained by Genotyping-by-Sequencing (GBS). A moderately high total diversity, heterozygotes deficit and inbreeding were found. Furthermore, we find three distinct genetic clusters (GC1, GC2 and GC3) with clear geographic correspondence to Amazonian, Andean, and Caribbean Colombian regions, a substantial phenotypic correlation with root bitterness and a greater differentiation between clusters than typically found in global scale studies. Each genetic cluster exhibits distinctive selection signatures reflecting region specific adaptations. GPI-anchor biosynthesis and chitin catabolism in Amazonian bitter cassava (defense against pathogens), oxidative stress response in Andean cassava (adaptation to highland conditions) and trehalose biosynthesis, cyano-amino acid metabolism and tuberization accumulation in Caribbean sweet cassava (drought tolerance, altered cyanogen processing and tuberization characteristics). These signatures align with phenotypic differentiation between bitter and sweet cultivars. These analyses highlight Colombia as a unique diversification core where environmental challenges and cultural practices have structured cassava diversity, underscoring the importance of integrated conservation strategies that preserve both genetic resources and the traditional knowledge systems that sustain them.