Yield potential,pharmaceutical compounds production and stress tolerance capacity are 3 classes of traits that determine the quality of medicinal plants.The autotetraploid Isatis indigotica has greater yield,higher bioactive lignan accumulation and enhanced stress tolerance compared with its diploid progenitor.Here we show that the transcription factor IiWRKY34,with higher expression levels in tetraploid than in diploid I.indigotica,has large pleiotropic effects on an array of traits,including biomass growth rates,lignan biosynthesis,as well as salt and drought stress tolerance.Integrated analysis of transcriptome and metabolome profiling demonstrated that IiWRKY34 expression had far-reaching consequences on both primary and secondary metabolism,reprograming carbon flux towards phenylpro-panoids,such as lignans and flavonoids.Transcript-metabolite correlation analysis was applied to construct the regulatory network of IiWRKY34 for lignan biosynthesis.One candidate target Ii4CL3,a key rate-limiting enzyme of lignan biosynthesis as indicated in our previous study,has been demonstrated to indeed be activated by IiWRKY34.Collectively,the results indicate that the differen-tially expressed IiWRKY34 has contributed significantly to the polyploidy vigor of I.indigotica,and manipulation of this gene will facilitate comprehensive improvements of I.indigotica herb.