Transcriptome and metabolome analyses revealed different salt tolerance pathways in leaves and roots of Rosa rugosa Thunb.

Rosa rugosa Thunb., mainly distributed on the coast in China, has strong salt tolerance, making it a good material to study the salt tolerance mechanism of plants. This study showed that under 200 mM NaCl stress, the activities of superoxide dismutase (SOD) and peroxidase (POD), and soluble sugar content, as well as malondialdehyde (MDA) content in R. rugosa roots and leaves first increased and then decreased. The differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) enriched in the leaves were significantly more than those in the roots, and they played a dominant role in the response to salt stress. Combined metabolome and transcriptome analyses showed that starch and sucrose metabolism, tryptophan metabolism and purine metabolism played essential roles dealing with salt stress in root. The flavonoid biosynthesis pathway and glycerophospholipid metabolism pathway were significantly enriched in the leaves, which improved antioxidant ability. In addition, abscisic acid (ABA) accumulated in the leaves and roots and was the most important anti-salt hormone in R. rugosa. The study elucidated the molecular mechanism underlying the response of R. rugosa to salt stress and supplied breeding of salt-tolerant R. rugosa with theoretical support.