Stage-specific metabolic responses of piquin peppers to colored shading nets across fruit maturation revealed by 1H NMR metabolomics

In Mexico, piquin peppers ( Capsicum annuum L. var. glabriusculum ) are highly valued for their distinctive flavor, pungency, and bioactive phytochemicals. Under cultivated conditions, production commonly occurs under shade structures; however, the biochemical consequences of shade nets on fruit metabolism remain poorly characterized. This study evaluated how shade nets of different colors influence the metabolic composition of piquin pepper fruits during ripening. Untargeted 1 H NMR-based metabolomics profiling was employed to characterize metabolic changes associated with fruit maturation and shade-net environments. This approach enabled the simultaneous detection of primary and secondary metabolites, revealing subtle biochemical responses to different light-filtering conditions. Fruit maturation was the dominant determinant of the metabolic profile. Immature fruits contained higher levels of amino acids and nucleosides, whereas mature fruits accumulated greater concentrations of organic acids, sugars, proline, and capsaicinoids. Shade-net treatments produced moderate but measurable metabolic shifts. In immature fruits, aspartate concentrations decreased under black and gray nets, while 2,3-butanediol increased under black nets. In mature fruits, capsaicin concentrations were higher under blue and gray nets than under other treatments. These fruits also exhibited increased levels of alanine, acetate, glutamine, and signals associated with histidine/formate metabolism. Overall, shade nets did not substantially alter the global metabolic structure but induced targeted adjustments in pathways associated with nitrogen metabolism and secondary compound accumulation. The developmental stage was the dominant determinant of metabolic composition in piquin peppers. In contrast, shade-net color exerted secondary but relevant effects on specific metabolites, including capsaicinoids and nitrogen-related compounds. These findings indicate that shading strategies can subtly modulate the biochemical profile of peppers without disrupting the overall metabolic progression during ripening, providing insights into optimization strategies of protected cultivation systems and improving fruit quality.