Field-Zone-Associated Transcriptomic and Metabolic Divergence Despite Nearly Identical Observed Chlorophyll in an Agrivoltaic Tea Setting

Abstract

Background/Objectives: Similar leaf chlorophyll in agrivoltaic tea fields may conceal molecular divergence. Methods: We reanalysed physiology, RNA sequencing and metabolomics from five field zones (three plant-level replicates each), prioritizing T2 versus T3. Missing plot maps and independent installation replicates limited inference to zone associations. Results: T2 and T3 had nearly identical mean total chlorophyll (0.50495 versus 0.50309 mg g−1; Welch p = 0.920), whereas T2 had higher carotenoids, total sugars, alkaloids, phenols and flavonoids; all five differences had Benjamini–Hochberg false discovery rate (FDR) < 0.05 across 50 physiological tests. Relative to the open-sun control (CK), T2 and T3 had 7 and 6857 differentially expressed genes and 35 and 523 differential unique metabolite profiles, respectively. Omitting one sample from each of T2, T3 and CK yielded 27 combinations, all showing greater transcriptome and metabolome displacement in T3. After adjustment for the leading whole-omics component, exact within-zone permutation supported sample-pattern coupling for glycolysis and porphyrin metabolism (Benjamini–Hochberg FDR = 0.0288 for each). In comparison with four public tea datasets, T1 showed the strongest descriptive rank concordance; T3 showed little concordance. Conclusions: Similar chlorophyll means coexist with divergent molecular profiles. These observational results do not establish effects of photovoltaic hardware.