Integrated transcriptomic and metabolomic analyses reveals the molecular bases of alfalfa regrowth processes of new shoots after cutting under different water and nitrogen availability

Alfalfa regrowth is a complex process that is frequently constrained by deficits in water and N fertilisers after cutting. However, the transcriptomic regulatory networks and primary metabolic changes during regrowth are largely unknown. The alfalfa regrowth biomass responses to water deficiency and water deficiency supplied with N fertilisers and corresponding transcriptional and primary metabolic changes in new leaves and roots were systematically explored at 9 and 14 d after cutting. Water deficiency significantly decreased the alfalfa regrowth biomass. Integrated transcriptomic and metabolomic analysis demonstrated that osmoprotection related genes, sucrose and starch metabolic pathways, hormone biosynthesis and signalling pathways, and key transcription factors in new leaves and roots are responsible for alfalfa regrowth under water deficiency. Furthermore, alfalfa regrowth biomass was significantly improved in the presence of N fertilisers under water deficiency through multigene network coordination and metabolic pathway rearrangement. Interestingly, differentially expressed genes expression occurred predominantly in roots at 9 d after cutting, while it mainly occurred in the new leaves at 14 d after cutting. This study revealed the complex molecular mechanisms of alfalfa regrowth and provided theoretical support for optimal irrigation and N fertiliser strategies that will achieve maximum biomass of alfalfa in dryland farming areas.