Integrative physiological, metabolomic and transcriptomic analysis reveals nitrogen preference and carbon and nitrogen metabolism in blackberry plants

Nitrogen (N) is an indispensable element for plant growth and development. To understand the regulation of underlying carbon (C) and N metabolism in blackberry plants, we performed integrated analyses of the physiology, metabolome and transcriptome. Blackberry plants were subjected to no N, nitrate (NO3⁻)-N, ammonium (NH4+)-N and urea treatments. Our results showed that the NH4⁺-N treatment yielded higher values for the biomass, chlorophyll, antioxidants, N contents and antioxidant enzyme activities, as well as lower levels of free radicals and the C/N ratio compared with other treatments. Transcriptome analysis showed that different N forms significantly affected photosynthesis, flavonoid biosynthesis and the TCA cycle. Metabolome analysis indicated that the levels of lipids, carbohydrates, flavonoids and amino acids were markedly changed under different N treatments. Integrated transcriptomic and metabolomic data revealed that amino acids, including proline, arginine, L-isoleucine, L-aspartate, threonine, and L-glutamate, played important roles in maintaining normal plant growth by regulating N metabolism and amino acid metabolism. Overall, blackberry plants preferentially take up NH4⁺-N. Under the NH4⁺-N treatment, N assimilation was stronger, flavonoid biosynthesis was decreased, and the promoting influence of NH4⁺-N on N metabolism was better than that of NO3⁻-N. However, the NO3⁻-N treatment enhanced the C/N ratio, accelerated the process of C metabolism and increased the synthesis of flavonoids, thereby accelerating the flow of N metabolism to C metabolism. These results provide deeper insight into coordinating C and N metabolism and improving N use efficiency in blackberry plants.