Transcriptomics study on 49 African Cassava genotypes

Cassava (Manihot esculenta) is a critical staple food for smallholder farmers in the tropics, particularly in Asia and Sub-Saharan Africa. While high yield is still the most desirable trait for farmers, nutritional value has gained importance in cassava breeding programs. However, a clear negative correlation between provitamin A and starch accumulation represents a major breeding challenge. The inverse relationship between starch and carotenoid levels, evident in both conventional and genetically modified cassava plants, suggests no direct genomic link between the two traits. Instead, metabolic competition between different carbon pathways could account for this negative correlation. In this study, we performed comprehensive phenotypic, metabolic, and transcriptional analyses of 49 African cassava genotypes with varied starch and provitamin A levels to identify factors related to the differential starch accumulation. Considering the varieties carotenoid levels as confounding effect for their starch production, we found that the yellow- and white-fleshed storage roots did not differ in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites linked to myo-inositol synthesis and cell wall component production were significantly enriched in high provitamin A genotypes. This suggests that yellow-fleshed varieties, compared to white-fleshed varieties, allocate more carbon towards the synthesis of raffinose and cell wall components, a finding that is further underpinned by a significant increase in the starch-free residue to total dry yield ratio in yellow compared to white storage roots.