TABLE 2.

Regulatory and structural genes shown to be involved in the biosynthesis of anthocyanin and proanthocyanidin in rice.

Locus	Allelic locus	Gene name	Locus ID		CHRXa	Pericarp	References
			Rice Annotation Project (RAP)	Rice Genome Annotation Project (MSU)
Regulatory genes
Kala1	Rd	OsDFR	Os01g0633500	LOC_Os01g44260	1	Red and black	Furukawa et al., 2006; Shih et al., 2008; Maeda et al., 2014; Sun et al., 2018
	Pp				1	Red and black	Caixia and Qingyao, 2007
Kala3		OsMYB3	Os03t0410000	LOC_Os03g29614	3	Black	Maeda et al., 2014
Kala4	Plw	OSB1/Pb/Ra	Os04g0557800	LOC_Os04g47080	4		Hu et al., 1996; Sakamoto et al., 2001; Caixia and Qingyao, 2007; Sakulsingharoj et al., 2016
		OSB2	Os04g0557500	LOC_Os04g47059	4		Sakamoto et al., 2001; Sakulsingharoj et al., 2014; Oikawa et al., 2015
Rc	Rc-s	bHLH	Os07g0211500	LOC_Os07g11020	7	Red	Sweeney et al., 2006
	Rc				7	Red	Furukawa et al., 2006
	rc				7	White	Furukawa et al., 2006; Sweeney et al., 2006
	Rc-g				7	Red	Brooks et al., 2008
	Rcr				7	Red	Ferrari et al., 2015
	Rc-gl				7	White	Gross et al., 2010
Chromogen		OsC1	Os06g0205100	LOC_Os06g10350	6	Black	Saitoh et al., 2004; Rachasima et al., 2017; Sun et al., 2018
Structural genes
Chalcone synthetase (CHS)		OsCHS1	Os11g0530600	LOC_Os11g32650	11	Common intermediate	Shih et al., 2008
		OsCHS2	Os07g0214900	LOC_Os07g11440	7	Common intermediate
Chalcone isomerase (CHI)		OsCHI	Os03g0819600	LOC_Os03g60509	3	Common intermediate	Shih et al., 2008
Flavanone 3-hydroxylase (F3H)		OsF3H-1	Os04g0662600	LOC_Os04g56700	4	Common intermediate	Kim et al., 2008
		OsF3H-2	Os10g0536400	LOC_Os10g39140	10
		OsF3H-3	Os04g0667200	LOC_Os04g57160	4
Flavanone 3′-hydroxylase (F3′H)		OsF3′H	Os10g0320100	LOC_Os10g17260	10	Common intermediate	Shih et al., 2008
Leucoanthocyanidin reductase (LAR)		OsLAR	Os03g0259400	LOC_Os03g15360	3	Black rice	Kim et al., 2015
Anthocyanidin synthase (ANS)		OsANS1	Os01g0372500	LOC_Os01g27490	1	Black rice	Shih et al., 2008
		OsANS2	Os06g0626700	LOC_Os06g42130	6
UDP-glycosyltransferase (UF3GT)		OsUGT	Os06g0192100	LOC_Os06g09240	6	Black rice	Yoshimura et al., 2012
			Os07g0148200	LOC_Os07g05420	7	Black rice
Anthocyanin reductase (ANR)		OsANR	Os04g0630800	LOC_Os04g53850	4	Black rice	Kim et al., 2015

^aCHRX: chromosome.