Comparative transcriptome and physiological analyses of the Polygonatum odoratum (Mill.) Druce rhizome responses to continuous cropping

Polygonatum odoratum, a valuable medicinal herb, faces severe cultivation constraints due to continuous cropping (CC) obstacles, yet the physiological and molecular mechanisms in its rhizome remain unclear. This study integrates physiological and transcriptomic analyses comparing CC and first-cropping plants. Under CC stress, rhizomes exhibited reduced diameter, root length, and root number, along with decreased antioxidant enzyme activities and polysaccharide content, but increased malondialdehyde levels and 3 types of phenolic acids. RNA-seq identified 3357 upregulated and 1215 downregulated DEGs. KEGG analysis revealed downregulation in plant hormone signal transduction, particularly in IAA-related genes, while the JA, CTK, and ABA pathways, along with key carbohydrate metabolism processes, were upregulated. Moreover, exogenous NAA application promotes the root growth in the rhizome of P. odoratum. These results uncover hormone signaling reprogramming and metabolic shifts underlying CC responses, offering novel insights and a theoretical basis for mitigating cropping obstacles in medicinal plants.