Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

Table 3 Determination of loci for eating and cooking qualities in japonica subpopulation

Traits	Associated Markers	Position (kb)	Chr.	MAF	2015		2016		Linked Gene
Traits	Associated Markers	Position (kb)	Chr.	MAF	P value	R²	P value	R²	Linked Gene
AC	Wx-S3	1765	6	0.058	1.81E-25	21.86	3.12E-28	20.87	Wx^mp
AC	RM550	12,464	2	0.353	9.36E-06	5.14	1.40E-05	4.39
ASV	SSIIa-S1	6747	6	0.035	3.84E-04	3.55			SSIIa
	SSIIa-S2	6747	6	0.029	4.27E-05	5.56			SSIIa
	RM5331	7177	6	0.052	3.54E-04	3.6			SSIIa linked
	RM1375	16,716	10	0.012	9.23E-04	5.39			SSIIb linked
PV	RM302	32,988	1	0.006			7.44E-04	3.54
	RM5791	10,747	2	0.012			5.27E-04	2.59
	RM420	30,092	7	0.017			9.88E-04	2.92
HPV	SBE4-S2	20,238	4	0.012	4.56E-05	5.04			SBE4
	AGPLar	28,877	5	0.006	3.84E-04	4.87			AGPLar
	Wx-S3	1765	6	0.058	3.19E-04	3.97	9.00E-04	2.58	Wx^mp
	STS9–1	10,861	9	0.012	3.28E-04	3.96
BDV	Wx-S3	1765	6	0.058			8.16E-05	4.43	Wx^mp
BDV	RM276	6230	6	0.012			8.38E-04	4.79	SSIIa linked
CPV	SBE4-S2	20,238	4	0.012	2.50E-04	4.34			SBE4
CPV	Wx-S3	1765	6	0.058	1.22E-10	12.05	3.17E-07	6.34	Wx^mp
SBV	RM550	12,464	2	0.353	8.93E-05	4.46
	Wx-S3	1765	6	0.058	4.53E-08	8.11	7.74E-10	9.37	Wx^mp
	RM336	21,872	7	0.018			3.67E-04	6.05
CSV	RM550	12,464	2	0.353	3.49E-04	4.03
CSV	Wx-S3	1765	6	0.058	5.20E-14	15.48	1.71E-11	12.36	Wx^mp
PeT	SBE4-S2	20,238	4	0.012	8.65E-04	3.45			SBE4
	Wx-S3	1765	6	0.058	4.78E-06	6.32	2.93E-05	4.73	Wx^mp
	RM276	6230	6	0.012			2.79E-05	6.42	SSIIa linked
Ptemp	SSIIIb-S1	31,759	4	0.017	1.82E-06	7.51			SSIIIb
	RM276	6230	6	0.012	2.73E-05	6.85	7.12E-10	9.12	SSIIa linked
	SSIIa-S1	6747	6	0.035			6.06E-05	3.48	SSIIa
	SSIIa-S2	6747	6	0.029			3.68E-07	6.17	SSIIa
	RM5688	1716	9	0.006			9.46E-05	4.52

MAF: Minor allele frequency
R² represents the proportion of phenotypic variation explained by each associated locus

ISSN: 2730-6844