Primers for qRT-PCR analysis.

<div><p><i>Fritillariae thunbergii</i> Bulbus (FTB) is a traditional Chinese medicine that has been widely cultivated for its expectorant, antitussive, antiasthmatic, antiviral, and anticancer properties. The yield and quality of <i>F</i>. <i>thunbergii</i> are influenced by cultivation conditions, such as the use of fertilizers. However, the optimal type of fertilizers for maximum quality and yield and underlying mechanisms are not clear. We collected <i>F</i>. <i>thunbergii</i> using raw chicken manure (RC), organic fertilizer (OF), and plant ash (PA) as the base fertilizer in Pan’an County, Jinhua City, Zhejiang Province as experimental materials. The combined results of HPLC-ELSD detection and yield statistics showed that the <i>F</i>. <i>thunbergii</i> with OF application was the best, with the content of peimine and peiminine reaching 0.0603% and 0.0502%, respectively. In addition, the yield was 2.70 kg/m<sup>2</sup>. Transcriptome analysis indicated that up-regulation of the ABA signaling pathway might promote bulb yield. Furthermore, putative key genes responsible for steroidal alkaloid accumulation were identified. These results provided guiding significance for the rational fertilization conditions of <i>F</i>. <i>thunbergii</i> as well as the basis for the exploration of functional genes related to the alkaloid biosynthesis pathway.</p></div>