Multi-omics characterisation of cubio (Tropaeolum tuberosum, Tropaeolaceae)

Cubio, mashua, or isaño (Tropaeolum tuberosum, Tropaeolaceae) is an Andean edible tuber with notable agroecological properties, including tolerance to low temperatures, adaptability to nutrient-poor soils, high productivity, and resistance to pests. In addition to its agronomic value, cubio possesses important nutraceutical and medicinal properties, as it is a source of fiber, proteins, phosphorus, magnesium, provitamin A, and vitamin C, as well as various bioactive compounds such as polyphenols, glucosinolates and isothiocyanates, fatty acids, and alkylamides. Previous, but scarce, studies have reported high morphological diversity, primarily found in tuber traits, along with moderate-to-high levels of genetic variation. Comparative analyses have also revealed marked metabolic differences among tuber morphotypes. Despite these valuable attributes and wide diversity, cubio remains relatively unattractive to consumers and consequently has limited economic relevance compared with other Andean tubers. Therefore, further basic research is needed to better characterise, utilize, and valorise this Andean native crop by identifying the genetic and biochemical bases underlying its phenotypic diversity and metabolic potential. This study, started in 2021, was aimed at generating genomic resources for this species by characterizing the genetic and phenotypic diversity of a collection of tuber morphotypes, mainly collected in smallholder farms of Colombia. First, a high-quality, functionally annotated draft genome will be generated to serve as one of the first references for this crop. This genomic resource will enable downstream analyses of genetic diversity through SNP-based genotyping using whole-genome sequencing (WGS) of the members of this collection. In addition, phenotypic variability will be investigated through transcriptomic profiling using RNA sequencing (RNA-seq) of three contrasting tuber morphotypes. These analyses will allow the identification of the genetic background, molecular mechanisms, and secondary metabolic pathways that contribute to the accumulation of metabolites in the tubers underlying their high phenotypic diversity. Overall, this project proposes an integrated multi-omic approach to comparatively characterize genetic and phenotypic diversity among cubio morphotypes collected in Andean regions of Colombia and Bolivia. In the long term, these findings may facilitate the identification of morphotypes with desirable metabolite accumulation profiles, opening opportunities for the improvement of traits of interest for producers, consumers, and the agro-industrial sector, and ultimately contributing to the greater valorisation of this native Andean tuber.