Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

Table 5

Overview of genic SNPs in the genes encoding enzyme of flavonoid biosynthetic pathway. All genes were categorized into general phenylpropanoid, early biosynthetic genes, late biosynthetic genes, and transcription factor (bHLH (Kala4 and Rc), R2R3-MYB).

Group of genes	Genes name	Total SNPs	Total SNPs (%)
General phenylpropanoid genes	Phenylalanine ammonia-lyase (PAL); Cinnamate-4-hydroxylase (C4H); 4-Coumarate ligase (4CL)	511	28
Early biosynthetic genes (EBGs)	Chalcone synthase (CHS); Chalcone isomerase (CHI); Flavanone 3-hyroxylase (F3H); Flavanone 3-hydroxylase (F3H)	463	26
Late biosynthetic genes (LBGs)	Dihydroflavonol reductase (DFR); Leucoanthocyanidin reductase (LAR); UDP-glucose flavonoid 3-O-glucosyl transferase (UGT); Leucoanthocyanidin oxidase (LDOX)	675	37
Transcription factors (TFs)	Basic helix-loop-helix (bHLH); R2R3-MYB	160	9