Transcriptomic analysis of saffron at different flowering stages using RNA sequencing uncovers cytochrome P450 genes involved in crocin biosynthesis

Saffron is a well-known Chinese traditional herb, and crocin biosynthesis is related to the yield and quality of saffron. This study aimed to screen differentially expressed genes (DEGs) in saffron at different flowering stages and identify cytochrome P450 (CYP) genes involved in crocin biosynthesis. Saffron samples at different flowering stages were used for RNA sequencing, and DEGs between the samples at three days before the flowering stage (− 3da) and two days after the flowering stage (+ 2da) were screened. Thereafter, significantly differentially expressed CYP genes were identified, and CYP gene expression at different flowering stages and in various tissues of saffron was determined using real-time quantitative polymerase chain reaction (RT-qPCR). After sequencing and analysis, 1508 DEGs between the samples at − 3da and + 2da were identified, including 487 upregulated and 1021 downregulated genes, which were enriched in 16 biological processes, 5 cellular components, 3 molecular functions, and 11 KEGG pathways, including protein processing in endoplasmic reticulum, pentose and glucuronate interconversions, starch and sucrose metabolism, estrogen signaling pathway, and mitogen-activated protein kinase signaling pathway. In addition, 12 significantly differentially expressed CYP genes were identified. The RT-qPCR results showed that CYP76C4 , CYP72A15 , CYP72A219 , CYP97B2 , CYP714C2 , CYP71A1 , CYP94C1 , and CYP86A8 were all expressed in the pistils, and CYP72A219 , CYP72A15 , CYP97B2 , CYP71A1 , and CYP86A8 were highly expressed in the pistils. Our study established a transcriptome library of saffron and found that CYP72A219 , CYP72A15 , CYP97B2 , CYP71A1 , and CYP86A8 may be candidates involved crocin biosynthesis in saffron.