A resource for improving the quality and yield of Crocus sativus stigma

Crocus sativus is an autotriploid hybrid with many medicinal benefits from its stigmas. The crocin level, along with the number and weight of flowers, greatly affects the quality and yield of the stigmas. However, limited resources are available for studying the key genes responsible for these important agronomic traits. This study presents the first complete assembly of the C. sativus genome. It uncovers genomic rearrangements among the three chromosome sets and the loss of two large syntenic regions, which may influence the rates of genome divergence. By combining this new genome assembly with time-course mRNA transcriptome analyses across multiple developmental stages of stigma and flower bud tissues, we identified key candidate genes involved in carotenoid biosynthesis and flowering. We then experimentally verified the specific role of one gene, CsFT3 - like , discovering that it acts as a positive regulator of flowering and pistil weight. Lastly, the putative flowering regulatory network in C. sativus was examined and compared with that of Arabidopsis, revealing many additional potential flowering-related genes that may function at distinct stages of development. The present study provides a valuable resource for understanding the genomic evolution of C. sativus and offers insights for enhancing its stigma quality and yield. • The first complete genome assembly of the autotriploid saffron crocus. • Identification of biosynthetic genes of carotenoid through time-course RNA-seq. • Identification of flowering genes via time-course RNA-seq. • The CsFT3-like protein is a positive regulator of flowering and pistil weight.