Deciphering podophyllotoxin-mediated defense against downy blight in Litchi chinensis Sonn. via integrated metabolomics and transcriptomics

Lychee (Litchi chinensis Sonn.) is a commercially important subtropical fruit. Lychee downy blight (LDB), caused by Peronophythora litchii, poses a major threat to lychee production. Here, we identified the LDB-resistant cultivar Yurong (YR) and the susceptible cultivar Guiwei (GW) from 288 global lychee germplasms. Widely targeted metabolomics analysis revealed a striking accumulation of podophyllotoxin (PTOX) in YR. Both in vitro and in vivo assays demonstrated that PTOX effectively inhibited the growth of P. litchii. Further investigation identified LcOMT1 as a key gene encoding an O-methyltransferase (OMT) in the phenylpropanoid pathway. In resistant cultivars, a 773-bp insertion mutation (Hap3 haplotype) in the LcOMT1 promoter enhanced its transcriptional activity. Transgenic approaches using hairy roots in lychee showed that the overexpression of either LcOMT1 or the Hap3 haplotype led to increased PTOX biosynthesis and enhanced resistance to P. litchii. These results demonstrate that the Hap3-mediated upregulation of LcOMT1 drives PTOX accumulation, establishing a crucial defense mechanism against LDB. This study provides new insights into the genetic and metabolic regulatory network underlying lychee resistance to LDB. This study may also lay a theoretical foundation for the development of PTOX-based biopesticides and offer valuable genetic resources for breeding LDB-resistant lychee cultivars.