Allium cepa var. aggregatum Raw sequence reads. Allium cepa var. aggregatum

Potato onion is a plant allelopathic to tomato seedlings; however, the mechanisms underlying the allelopathic effect remain unknown. Here, we examined the effects of potato onion leaf volatiles and leachates on tomato seedling growth, and performed a transcriptomic comparison of two potato onion cultivars with different allelopathic potentials (‘Suihua’: high allelopathic potential; ‘Qitaihe’: lower allelopathic potential). Potato onion leaf volatiles and leachates decreased the stem length, but increased the shoot dry matter of tomato seedlings. Transcriptomic analysis showed that 640 genes were differentially expressed (DEGs) between ‘Suihua’ and ‘Qitaihe’. DEGs related to photosynthesis, energy metabolism, and hormone metabolism were upregulated in ‘Suihua’ compared to that in ‘Qitaihe’, whereas genes related to phenylpropanoid metabolism were downregulated, indicating lower phenolic acid accumulation, and thus lower allelopathic inhibitory effects. In conclusion, the allelopathic effects of potato onion cultivars on tomato seedlings may be attributable to differences in photosynthesis, plant hormone, energy, and phenylpropanoid metabolism.