Transcriptomic profiling reveals color variation mechanism of Fritillaria cirrhosa for the molecular plant breeding

Fritillaria cirrhosa is a remarkably representative endangered species on the plateau, and its phenotype has undergone dramatic alterations due to global climate change and habitat destruction. However, the mechanism behind the phenotypic change associated with color variation has not been characterized, and subsequent physiological responses are still unknown. We investigated different phenotypes of cultivated F. cirrhosa and conducted a comprehensive transcriptomic analysis. Their agronomic traits, photosynthetic parameters, and the content of pharmaceutical ingredients were also compared. In the transcriptomic profiling, the purple phenotype had 754 up-regulated and 980 down-regulated genes compared with the green F. cirrhosa, in which a total of 37 significant differential expression genes (DEGs) regulated the anthocyanin biosynthesis by coding 6 vital enzymes (C4H, F3′H, ANS, DFR, DFT, and BA1). These DEGs were key genes responsible for the form of the purple phenotype of F. cirrhosa. Moreover, 10 DEGs were observed to be related to biotic and abiotic stress responses, such as regulation of defense response to bacterium and UV regulation in the actual unshaded field environment. The results of agronomic traits indicated that the purple phenotype exhibited a multitude of merits in plant height and stem diameter (p < 0.05), and produced more high-quality fruit and seeds, which demonstrated that the purple phenotype has high regeneration ability and potential resistance to cultivation conditions. Importantly, the content of total alkaloids as bioactive ingredients in medicinal bulbs of purple F. cirrhosa was significantly higher than that in the green phenotype by 57.14%. Overall, the present study not only reveals the potential mechanisms of phenotypic variation in F. cirrhosa but also contributes to a better understand adaptation of highland species related to ecological changes, as well as paves the way for the further breeding and large-scale cultivation of F. cirrhosa.