Nitrogen Source Affects the Composition of Metabolites in Pepper (Capsicum annuum L.) and Regulates the Synthesis of Capsaicinoids through the GOGAT–GS Pathway

Phytochemical analyses of pepper fruit metabolites have been reported; however, much less is known about the influence of different forms of nitrogen (N), which is critical for plant growth and fruit quality formation. The “Longjiao No. 5” variety (Capsicum annuum L.) grown in Northwestern China was profiled using liquid chromatography–mass spectrometry (LC–MS) coupled with multivariate data analysis to explore the composition of different metabolites in pericarp and placenta, and to investigate the effect of three ammonium (NH(4)(+)) to-nitrate (NO(3)(−)) ratios (0:100, 25:75, and 50:50). A total of 215 metabolites were obtained by qualitative analysis, where 31 metabolites were the major differential metabolite components of pepper fruits between placenta and pericarp, and 25 among N treatments. The addition of ammonium up-regulated carbohydrates, such as α-lactose and sucrose, as well as phenylalanine lyase (PAL) of placenta tissue. The supply of 25% NH(4)(+)–N and 75% NO(3)(−)–N exhibited a relatively higher levels of ascorbic acid in pericarp and amino acids, capsaicin, and dihydrocapsaicin in placenta, and led to higher fruit weight among the ammonium-to-nitrate ratios. The expression and activities of glutamic acid synthetase (GOGAT) and glutamine synthetase (GS) that are involved in ammonium assimilation were affected by adjusting the ammonium–N proportion, and they were significantly positively correlated with capsaicin, dihydrocapsaicin contents, capsaicinoid synthetase (CS), as well as the relative expression levels of genes related to capsaicinoid biosynthesis, such as acyltransferase 3 (AT3) and acyl-ACP thioesterase (FatA).