The discovery of novel botanical pesticides as a preferred alternative to synthetic pesticides is regarded as an environmentally friendly strategy, yet it remains a great challenge due to limited insights into the synthesis and accumulation of active ingredient intermediates. Herein, we demonstrate the use of gold nanoparticle (AuNP)-assisted laser desorption/ionization mass spectrometry imaging (LDI-MSI) for the tissue-specific distribution and spatiotemporal accumulation effect of rotenone and active ingredient intermediates in its biosynthetic pathway within the roots of Derris elliptica. The MSI results revealed that rotenone was mainly concentrated in the epidermis, cortex, and xylem in the first two years and began to accumulate in the phloem since the 3rd year. Meanwhile, the rotenone contents increased in the epidermis, cortex, and xylem in the 4th year and finally decreased in the 5th year. The ultra-performance liquid chromatography (UPLC) results revealed that there was a significant difference in rotenone content between the root and non-root bark (p < 0.05) except for the 1st year. It reached its maximum value at 9.71% in the root bark in the 4th year and 7.98% in the non-root bark in the 1st year, which was in accordance with the MSI results. Additionally, the active ingredient intermediates in the Hydroxylation/Methylation and Rotenoid Phases of the biosynthetic pathway of rotenone were concentrated in the root region. Taken together, the collective results provide the scientific guidance for the scientific cultivation of D. elliptica and the efficient extraction of botanical pesticides.
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