TABLE 3.

Quantitative trait loci identified for colored related traits, anthocyanin and proanthocyanidin.

No.	Population	Size	Markers	Trait category	QTLs/QTNs	Closest structural and/or regulatory genes	Chromosome	Effect (%)	References
1	RILs	238	162 RFLP and 48 SSRs	Flour color	9		1,3,4,5,6,7,8	4.3–25.4	Tan et al., 2001
					L* (3)		5,6,8	4.5–15.7
					a* (2)		4,7	6.9–10.5
					b* (4)		1, 3,6,8	4.3–25.4
2	BRILs	182	162 RFLP	Degree of red coloration	4		1,7,9,11	2.1–83.7	Dong et al., 2008
					qDRC-1*	Rd	1	3.6–3.7
					qDRC-7*	Rc	7	75.9 -83.7
					qDRC-9		9	2.1–3.2
					qDRC-11		11	3.3–3.4
3	RILs	182	126 SSRs	Anthocyanin and proanthocyanidin	21		1,2,3,7,8,10,12	3.8–34.8	Xu et al., 2017
					ANC (8)		1,2,3,7,10	8.8–34.8
					PAC (13)		1,2,7,8,10,12	3.8–17.0
4	Diversity panel	416	100 SSRs and 10 gene markers	Grain color	25		1,4,6,7,8,9,10,11,12	1.39–86.68	Shao et al., 2011
					L* (3)	Ra, Rc	4,7,10	4.96–31.23
					a* (8)	Ra, Rc	1,4,7,8,9,11,12	1.51–19.65
					b* (6)	Ra	4,6,8,9,10	4.38–49.82
					c (3)	Ra	4,8,10	1.39–3.99
					H° (5)	Ra	4,6,8,9	5.4–86.68
				Phenolic and flavonoid content	10		4,7,8,9,10	2.64–39.67
					PC (4)	Ra, Rc	4,7,8,9	5.87–39.67
					FC (6)	Ra, Rc	4,7,8,9,10	2.64–35.35
5	Diversity panel	203	sequencing data	Pericarp color (PC)	4		7,10		Wang et al., 2016
					Rc-s	Rc-s	7
					qPc10	F3H	10
6	Diversity panel	244	122,785 SNPs	Red seed color	snp_07_6067391	bHLH			Butardo et al., 2017
7	Diversity panel	419	208,993 SNPs	Pericarp color_whole panel	763		1,3,4,7,8,10,11		Yang et al., 2018
						Rd	1
						MYB family transcription factors	10,11
						WD domain, G-beta repeat domain containing protein	8
				Pericarp color_indica	99
						MYB family transcription factors	10,11
						OsCHI	3
						Kala4	4
						Rc	7
						WD domain, G-beta repeat domain containing protein	8
						OsCHI	3
						Kala4	4
						Rc	7

RILs, recombination inbred lines; BRILs, backcross-recombinant inbred lines.