Non-Targeted Metabolomics Reveals the Metabolic Differentiation of Rice from Adjacent Small-Scale Producing Areas and Its Response to Climatic and Soil Factors

Geographical traceability of rice is critical for authenticity identification and quality control, yet it poses considerable challenges for tracing origins in adjacent small-scale producing areas. To explore the causes of metabolic differences and geographical traceability potential of rice from adjacent small-scale producing areas, non-targeted metabolomics combined with multivariate statistical analysis was employed to systematically investigate the metabolic profiles of rice from Panjin (PJ), Donggang (DG) and Yingkou (YK) in Liaoning Province. The characteristic metabolic markers for each producing area were screened, and the effects of climatic and soil factors as well as their interactive effects on grain metabolite composition were elucidated. The results showed that the partial least squares-discriminant analysis (PLS-DA) model established based on differential metabolites achieved acceptable discrimination among rice samples from the three regions. With variable importance in projection (VIP) > 2.0 as the screening threshold, the core characteristic markers of each producing area were determined: PJ is LPC 17:2, LPA 18:3, D-(+)-Arabitol, DG is 2′-Deoxyadenosine, LDGTS 18:2, and YK is LPE 17:2; the markers are mainly primary metabolites, including lipids, sugar alcohols and nucleotides. Sunshine duration, air humidity, wind conditions and soil layer temperature were highly correlated climatic drivers responsible for metabolic differentiation, and characteristic metabolic markers from different producing areas exhibited distinct meteorological response patterns. Soil physicochemical properties and mineral elements significantly affected the differential accumulation of metabolites, among which soil Sr element and organic matter exhibited crucial indicative significance for metabolic variation of rice in adjacent regions. Multi-factor interaction analysis verified significant synergistic coupling effects between regional climate and soil environment. Meteorological factors, including sunshine, wind and soil temperature, together with soil chemical factors involving organic matter, pH, Sr, K and Ca, were identified as core driving factors for the spatial differentiation of region-specific rice metabolites. The present study provides theoretical support at the metabolic level for the construction of a small-scale rice geographical traceability system and the mechanism research on the regional quality formation of rice.