Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

Table 2 Loci detected for eating and cooking qualities in the whole panel

	Chr.	Position	P value	MAF^a	R square^b
AAC	6	1765761	3.87 × 10⁻¹⁸	0.288	0.087
PRO	5	13312843	6.43 × 10⁻¹⁰	0.058	0.153
PRO	11	22562237	2.14 × 10⁻⁸	0.071	0.124
PV	5	7756614	3.40 × 10⁻⁶	0.235	0.070
PV	6	1765761	3.50 × 10⁻⁷	0.285	0.085
HPV	5	7944999	2.25 × 10⁻⁵	0.071	0.067
	6	1750498	1.37 × 10⁻⁶	0.077	0.088
	7	3359832	9.88 × 10⁻⁵	0.199	0.056
	9	17538294	7.44 × 10⁻⁵	0.071	0.058
CPV	1	31640680	1.05 × 10⁻⁶	0.277	0.087
	6	1750498	6.88 × 10⁻⁸	0.077	0.108
	9	17539188	1.53 × 10⁻⁶	0.071	0.084
BD	6	1765761	3.24 × 10⁻⁸	0.285	0.105
	7	1967427	4.05 × 10⁻⁶	0.173	0.071
	7	26540950	3.34 × 10⁻⁶	0.093	0.073
SB	4	24293919	3.44 × 10⁻⁷	0.166	0.069
	6	1765761	1.69 × 10⁻²	0.285	0.140
	7	1967427	2.11 × 10⁻⁷	0.173	0.072
	7	25326697	5.68 × 10⁻⁷	0.080	0.066
CS	1	30634461	2.42 × 10⁻⁶	0.261	0.041
	6	1765761	8.64 × 10⁻⁸	0.285	0.054
	9	15474876	4.59 × 10⁻⁶	0.215	0.039
PeT	1	31330790	1.39 × 10⁻⁷	0.265	0.087
	2	18003109	6.84 × 10⁻⁸	0.268	0.091
	5	8042699	1.06 × 10⁻⁶	0.173	0.074
	6	21450052	1.67 × 10⁻⁷	0.058	0.085
	8	21593355	2.64 × 10⁻⁷	0.270	0.082
PTemp	6	7002095	1.99 × 10⁻⁹	0.219	0.065
PTemp	12	17937512	1.59 × 10⁻⁶	0.157	0.041

a: MAF: minor allele frequency; b: R square was calculated by R square of model with SNP minus R square of model without SNP

ISSN: 1471-2164