Integrative Analyses of Metabolome and Transcriptome Reveals Apocarotenoid and Flavonoid Biosynthesis During Saffron (Crocus sativus L.) Stigmas Development

Previous research has primarily concentrated on elucidating the structural and functional aspects of genes involved in crocin biosynthesis. However, the complex changes in metabolites that affect nutritional value and their regulatory mechanisms during the stigma development of saffron (Crocus sativus L.) remain elusive. In this study, we delved into the functionality and complexity of the biosynthetic pathways for flavonoids and apocarotenoids in saffron, compounds that hold substantial nutritional significance. To explore the accumulation patterns and metabolic basis of apocarotenoid and flavonoid during saffron stigma development, widely targeted metabonomic and transcriptomic analyses in three (S1-S3) and four (S0-S3) developmental periods were conducted, respectively. The combined analysis of metabolism and transcriptome data showed that crocetin and flavonoids were mainly biosynthesized in the early red stage of stigma development (S1), and crocins were synthesized in the late red stage (S2). While the abscisic acid (ABA) biosynthesis pathway, a branch of crocetin metabolism, was particularly active at anthesis (S3), the synthesis of picrocrocin also increased during this stage. By employing weighted gene co-expression network analysis (WGCNA), key modules and hub genes associated with flavonoids and apocarotenoid biosynthesis were successfully identified. The starch and sucrose metabolism, as well as plant hormone signaling, are important for the synthesis of secondary metabolites, according to the enrichment analysis of key modules and functional analysis of several hub genes (G6Pep, UGE1, SBEI, IBR3, CKL2, and ARF15) from co-expression networks. In addition, a number of environmental stimuli were regarded as being significant, including flooding and red light. Our results provide new insights into the biosynthetic pathways and critical developmental stages that can be targeted for regulating the contents of secondary metabolites, ultimately enhancing the nutritional value and quality of saffron.