## 2 Results and Discussion
### Pearson's correlation Analysis and HCA  
Pearson's correlation analysis and HCA were performed to understand the relationships and metabolic network formed by the 110 identified metabolites (Figure 3 and Table S8). HCA revealed four metabolite clusters with strong correlations between metabolites and that were involved in closely related metabolic pathways (Figure 3A). Most amino acids, \(p\)-hydroxybenzoic acid, catechchin, and epicatechin were placed together in cluster 1 (Figure 3B). Cluster 2 contained most organic acids, sugars, and fatty acids. Cluster 3 consisted of terpenoids, policosanols, phenolic acids, and anthocyanins. Finally, cluster 4  
Figure 2: Orthogonal partial least squares-discriminant analysis (OPLS-DA) score and variable importance in the projection (VIP) plots derived from 110 metabolites of black, red, and non-pigmented (white) rice cultivars (**A**,**B**). A is comparison of non-pigmented rice and pigmented rice. B is comparison of black and red pigmented rice. The ellipse represents the Hotelling T2 with 95% confidence in the score plot. Plot annotation 1, C20-ol (Eicosanol); 2, C21-ol (Heneicosanol); 3, C22-ol (Docosanol); 4, C24-ol (Tetracosanol); 5, C26-ol (Hexacosanol); 6, \(\beta\)-Tocopherol; 7, \(\gamma\)-Tocopherol; 8, C27-ol (Heptacosanol); 9, C28-ol (Octacosanol); 10, \(\gamma\)-Tocotrienol; 11, \(\alpha\)-Tocopherol; 12, Cholesterol; 13, \(\alpha\)-Tocotrienol; 14, Campesterol; 15, C30-ol (Triacontonal); 16, Stigmasterol; 17, \(\beta\)-Sitosterol; 18, Lutein; 19, Zaxanthin; 20, \(\beta\)-Carotene; 21, Cyanidin-3-O-glucose; 22, Peonidin-3-O-glucose; 23, Catechin; 24, Epicatechin; 25, C16-0 (Palmitic acid); 26, C18.0 (Stearic acid); 27, C18:1 (Oleic acid); 28, C18:2 (Linoleic acid); 29, C18:3 (\(\alpha\)-Linolenic acid); 30, C20:0 (Arachidonic acid); 31, Pyrruvic acid; 32, Lactic acid; 33, Alanine; 34, Oxalic acid; 35, Valine; 36, Ethanolamine; 37, Lucine; 38, Glycerol; 39, Phosphoric acid; 40, Isoleucine; 41, Proline; 42, Glycine; 43, Succinic acid; 44, Fumaric acid; 45, Serine; 46, Threonine; 47, \(\beta\)-Alanine; 48, Malic acid; 49, Salicylic acid; 50, Methionine; 51, Aspartic acid; 52, Pyroglutamic acid; 53, \(\gamma\)-Aminobutyric acid; 54, Cysteine; 55, Threonine acid; 56, Glutamic acid; 57, \(p\)-Hydroxy benzoic acid; 58, Phenylalanine; 59, Asparagine; 60, Xylose; 61, Vanillic acid; 62, Glutamine; 63, Protocatechic acid; 64, Shikimic acid; 65, Citric acid; 66, Fructose; 67, Galactose; 68, Lysine; 69, Glucose; 70, \(p\)-Cumaric acid; 71, Tyrosine; 72, Mannitol; 73, Ferrulic acid; 74, Inositol; 75, Caffeic acid; 76, Tryptophan; 77, Sinapinic acid; 78, Sucrose; 79, Raffinose 80, 1-Butanol; 81, Pentanal; 82, 1-Pentanol; 83, Toluene; 84, Hexanal; 85, 1-Hexanol; 86, Ethlybenzene; 87, \(p\)-Xylene; 88, 2-Heptanone; 89, 2-Butylfuran; 90, Styrene; 91, Heptanal; 92, 2-Acetyl-1-pyrroline; 93, \(\alpha\)-Pinene; 94, 1-Heptanol; 95, Benzaldehyde; 96, 1-Octen-3-ol; 97, 2-Pentylfuran; 98, Octanal; 99, \(p\)-Cymene; 100, D-Limonene; 101, 3-Octen-2-one; 102, \(\gamma\)-Terpinene; 103, 1-Octanol; 104, Linalool; 105, o-Cymene; 106, Nonanal; 107, 1-Nonanol; 108, Naphthalene; 109, Decanal; 110, 1H-Indole. contained most volatiles, some tocopherols, and sugars (raftinose and mannitol). These four clusters revealed grouping of metabolites with closely related biosynthesis pathways. Furthermore, the metabolite concentrations in each cluster were positively correlated. Most metabolites in clusters 1 and 2 were primary metabolites, whereas those in clusters 3 and 4 were secondary metabolites. In addition, the levels of nitrogen compounds, such as amino acids, in clusters 1 and 2 were positively correlated; however, they were negatively correlated with the content of most carbon metabolites in the correlation matrix. Cellular carbon metabolism and nitrogen metabolism in plants are closely coordinated for optimal growth [24; 25].