Crocus sativus is a triploid sterile plant characterized by its long red stigmas, which produce and store significant quantities of the apocarotenoids crocetin and crocin, formed from the oxidative cleavage of zeaxanthin. Here, we investigate the accumulation and the molecular mechanisms that regulate the synthesis of these apocarotenoids during stigma development in C. sativus. We cloned the cDNAs for phytoene synthase, lycopene-b-cyclase, and b-ring hydroxylase from C. sativus. With the transition of yellow undeveloped to red fully developed stigmas, an accumulation of zeaxanthin was observed, accompanying the expression of CsPSY, phytoene desaturase, and CsLYCb, and the massive accumulation of CsBCH and CsZCD transcripts. We analyzed the expression of these two transcripts in relation to zeaxanthin and apocarotenoid accumulation in other Crocus species. We observed that only the relative levels of zeaxanthin in the stigma of each cultivar were correlated with the level of CsBCH transcripts. By contrast, the expression levels of CsZCD were not mirrored by changes in the apocarotenoid content, suggesting that the reaction catalyzed by the CsBCH enzyme could be the limiting step in the formation of saffron apocarotenoids in the stigma tissue. Phylogenetic analysis of the CsBCH intron sequences allowed us to determine the relationships among 19 Crocus species and to identify the closely related diploids of C. sativus. In addition, we examined the levels of the carotenoid and apocarotenoid biosynthetic genes in the triploid C. sativus and its closer relatives to determine whether the quantities of these specific mRNAs were additive or not in C. sativus. Transcript levels in saffron were clearly higher and nonadditive, suggesting that, in the triploid gene, regulatory interactions that produce novel effects on carotenoid biosynthesis genes are involved.Carotenoids are terpenoid compounds that are ubiquitous in nature. In all photosynthetic organisms, they carry out essential functions in light-harvesting systems and in photosynthetic reaction centers (Horton et al., 1996). In higher plants, carotenoids play additional roles in providing distinct yellow, orange, and red colors to certain organs, such as flowers and fruits, to attract animals for pollination and dispersal of seeds. In those tissues, unique carotenoids synthesized as secondary metabolites accumulate to high concentrations and are stored within the chromoplasts.All isoprenoids, including carotenoids, are derived from the ubiquitous C5 building blocks isopentenyl diphosphate and dimethylallyl diphosphate. These precursors can be synthesized through two different routes: the classical mevalonate pathway in the cytoplasm or the alternative nonmevalonate pathway in plastids (Rohmer et al., 1993;Arigoni et al., 1997). Metabolic cross-talk between the pathways can be observed under certain conditions (Hemmerlin et al., 2003). The plastidial pathway, now known as the 2-C-methyl-D-erythritol 4-phosphate pathway, has been fully elucidated by a combination of bi...