Moderate amounts of Se can promote crop growth, enhance stress resistance, increase yield, and improve nutritional quality. In the present study, kudzu seedlings were used as experimental materials, and their physiological indicators, antioxidant activity, nutritional components, and flavonoid content were measured after being treated with Na2SeO3 hydroponics. Transcriptome sequencing analysis was used to reveal the relevant genes involved in regulating the effects of exogenous Se on the content of Se-compounds and flavonoids in kudzu. The results indicated that treatment with 20 mg/L Na2SeO3 significantly increased stem and root lengths, dry and fresh weight, lateral root development, and chlorophyll b content. However, at higher concentrations (30–40 mg/L), lateral root abundance and chlorophyll levels decreased. Na2SeO3 treatment also augmented the antioxidant capacity and enhanced the content of major nutrients in kudzu seedlings. The total Se content in kudzu escalated with increasing Na2SeO3 concentration, with selenomethionine emerging as the primary organic-Se species. After treatment with Na2SeO3, the content of puerarin in both aboveground and underground parts decreased, while the content of total flavonoids increased. Daidzin increased in the roots. Differential expression gene analysis revealed that genes such as TRXB2, SYM, MMT1, and METE were involved in Se uptake and transformation in kudzu, while bZIP43 and WRKY47 played a role in flavonoid biosynthesis.
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