## 4 Conclusions  
In the present study, we conducted comprehensive metabolite profiling of 16 rice cultivars based on GC\(\times\)GC-TOF-MS, HS-SPME-GC-TOF-MS, GC-qMS, GC-FID, HPLC-MS, and HPLC-UV analyses. We identified 110 metabolites, including amino acids, organic acids, sugars, sugar alcohols, phenolic acids, flavonoids, anthocyanins, carotenoids, phytosterools, policosanols, tocopherols, fatty acids, and volatiles. BR contained high levels of metabolites from the terpenoid and phenylpropanol biosynthesis pathways, whereas RR only contained high levels of metabolites from the phenylpropanol biosynthesis pathway. Furthermore, WR contained low levels of secondary metabolites. Metabolome profiling was achieved by multivariate statistical analysis and PathVisio (metabolic pathway analysis), to determine the relationship between the rice cultivars and their metabolites. The multivariate and pathway analyses revealed correlations and metabolic differences associated with common and closely linked biosynthesis pathways. For the first time, the relationships and metabolic differences in terpenoid (monoterpenes, triterpenes, and tetraterpenes) content were demonstrated between non-pigmented and pigmented rice. Furthermore, the complex interactions between nitrogen and carbon metabolism of primary and secondary metabolites, via metabolic networks, in rice were demonstrated. These findings provide major new insights for understanding the metabolic networks in WR, BR, and RR, and should support future breeding programs for new rice cultivars. **Supplementary Materials:** The following are available online at [[https://www.mdpi.com/article/10.3390/metabo11060367/s1](https://www.mdpi.com/article/10.3390/metabo11060367/s1)]([https://www.mdpi.com/article/10.3390/metabo11060367/s1](https://www.mdpi.com/article/10.3390/metabo11060367/s1)), Figure S1: Principal component analysis (PCA) score plots (A) and loading plots (B) derived from 110 metabolites in 16 rice cultivars, Figure S2: Permutation test by OPLS-DA of pigmented rice and non-pigmented rice (A), and black rice and red rice (B), Figure S3: Phenotypes of 16 rice cultivars used in this study, Figure S4: GCxGC-TOF-MS analytical ion chromatogram (AIC) of hydrophilic compounds extracted from Dongjin (DJ), Figure S5: GC-FID chromatogram of fatty acid compounds from Suwon 505 (SW 505), Figure S6: HPLC chromatogram of carotenoid compounds from Heugnam (HN), Figure S7: HPLC chromatogram of anthocyanin compounds from Heuginju (HJJ), Figure S8: HPLC chromatogram of catechin and epicatechin from Aengmi (AM), Figure S9: HS-SPME GC-TOF-MS analytical ion chromatogram of volatile compounds from Heuginju (HJJ), Table S1: PLS-DA loading and VIP of variables, Table S2: Composition and content (ratio/g) of hydrophilic compounds in 16 pigmented rice cultivars, Table S3: Composition and content (ug/g) of catechin and epicatechin in 16 pigmented rice cultivars, Table S4: Relative retention times (RRT) and mass spectral data of lipophilic compounds as trimethylsilyl derivatives, Table S5: Composition and content (original peak areas \(\times\) 10\({}^{8}\)) of volatiles compounds in 16 pigmented rice cultivars, Table S6: VIP values of OPLS-DA (pigmented rice and non-pigmented rice), Table S7: VIP values of OPLS-DA (black rice and red rice), Table S8: Results of Pearson's correlation analysis, Table S9: Composition and content (ug/g) of anthocyanins in 16 pigmented rice cultivars, Table S10: Composition and content (ug/g) of lipophilic compounds, fatty acids, and carotenoids in 16 pigmented rice cultivars, Table S11: Pubchem CID and log\({}_{2}\)-transformed fold change (FC) (Log\({}_{2}\)FC) of metabolites, Table S12: Retention times (RT) and mass spectral data for volatile compounds, Table S13: Relative retention times (RRT) and mass spectral data for hydrophilic compounds as trimethylsilyl derivatives, Table S14: Relative retention times (RRT) and concentrations of fatty acid methyl ester (FAME) mixture and fatty acids, Table S15: Loadings of the variables in the first two principal components.