Β-carotene (BC) is the predominant carotenoid that accumulates in orange-fleshed sweetpotato storage roots and is a precursor of vitamin A. Starch is the most important carbohydrate in sweetpotato storage root and its composition, size, and shape of granules contributes to eating quality (Reeve 1967 Kitahara et al. Texture and sweetness determine the eating quality of sweetpotato, both of which depend on the quality and quantity of carbohydrates such as cellulose, hemicellulose, pectin, starch, and sugars (Reeve 1967). Additionally, such adapted varieties have specific textural characteristics after boiling that are preferred by local consumers. 1997), and consequently, these adapted varieties have been naturally selected to have relatively high starch content. As a major constituent of dry matter, starch accounts for about 75% of human caloric intake (Naeem et al. However, the crop had been historically grown in SSA as a food security crop with consumers preferring predominantly high dry matter types which are white-fleshed or yellow-fleshed and less nutritious (Low et al. Sweetpotato has been successfully demonstrated to provide provitamin A biofortification in sub-Saharan Africa (SSA) due to its ability to accumulate high levels of β-carotene, especially in the orange-fleshed types (Mwanga et al. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Using a biparental mapping population of 315 F 1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. Β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated.