Uncoupling the nexus between yield and carotenoid levels in sweet potato: development of improved cultivars and identification of key improvement genes

Sweet potato ( Ipomoea batatas (L.) Lam) is a globally important staple crop with high nutritional value, yet most commercial cultivars exhibit a trade-off between yield and carotenoid content. To address this limitation, we established a random open-pollinated polycross population using 27 elite varieties, conducted multi-stage field evaluation with phenotypic selection for yield and carotenoid content, and identified two F₃ clonally stabilized lines, XZ 8 − 1 and LS 9 − 1 with improved agronomic traits. XZ 8 − 1 showed a 40-fold increase in carotenoid content (µg/g FW) compared to its maternal line, while LS 9 − 1 maintained the high carotenoid levels of the maternal line but showed significantly improved yield. Molecular analysis of carotenoid biosynthetic genes identified IbGGPPS2 , a geranylgeranyl diphosphate synthase gene, that was highly expressed in high-carotenoid line XZ 8 − 1 and strongly correlated with carotenoid accumulation. Bacterial complementation assays confirmed that IbGGPPS2 encodes a protein with geranylgeranyl diphosphate synthase activity. Functional validation via heterologous expression in Arabidopsis and overexpression in sweet potato confirmed that IbGGPPS2 enhances carotenoid biosynthesis and plant growth, with transgenic lines showing 15–24% elevation, suggesting additional loci contribute to the large improvement in breeding lines. Given the hexaploid genome, IbGGPPS2 acts as a key contributor rather than a causal gene. Our findings provide a promising strategy for the simultaneous improvement of nutritional quality and yield in sweet potato breeding programs.