Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars

Table 2 SNPs associated with yield-related traits

							Candidate gene			Allele effect		QTL
Marker^a	Chr	Position (Mb)	Traits	Mean allele frequency of HY	–log10(P)	Permutation P	Name	OsID	Position (Mb)	PO-indica	PD	QTL-ID^b	Name	LOD	Interval or co-segregating marker
NIAS_Os_aa02003989			Surface area of unhusked seeds		5.12	0.001	-	-	-	19.68 ± 1.57	23.15 ± 3.26	108	gw2.1	3.25	RM250–RM208
	2	34.80	Length of unhusked seeds	0.62	4.67	0.003	-	-	-	8.26 ± 0.52	8.79 ± 0.76	362	-	3.99	C747–C1145
			1000-grain weight		5.48	0.003	-	-	-	22.54 ± 2.80	28.78 ± 4.94	-	-	-	-
NIAS_Os_ac07000274			Heading date		5.52	0.001				115.10 ± 7.62	128.67 ± 7.14	-	-	-	-
	7	10.15		0.41			Ghd7	Os07g 0261200	9.15
			Surface area of unhusked seeds		5.67	0.001				20.57 ± 2.27	18.05 ± 0.92	-	-	-	-
NIAS_Os_ab07000535	7	11.63	Surface area of unhusked seeds	0.47	4.83	0.003	-	-	-	20.53 ± 2.27	20.53 ± 2.27	-	-	-	-
NIAS_Os_ah08001148	8	19.61	Surface area of unhusked seeds	0.51	5.00	0.001	-	-	-	20.55 ± 2.26	19.37 ± 2.27	-	-	-	-
NIAS_Os_aa10003574	10	21.84	Length of unhusked seeds	0.21	4.52	0.004	-	-	-	8.26 ± 0.52	8.51 ± 0.70	211	-	7.98	RZ811–RG561
P0943	11	8.38	Number of panicles	0.46	4.90	0.004	-	-	-	218.67 ± 30.74	287.55 ± 45.63	-	-	-	-
NIAS_Os_aa12004348	12	9.10	Blast susceptibility	0.44	5.22	0.009	Pi–ta	Os12g 0281300	10.61	0.17 ± 0.84	2.35 ± 2.13	-	-	-	-
P0926	12	21.22	Blast susceptibility	0.48	5.55	0.002	-	-	-	0.07 ± 0.45	2.26 ± 2.18	383	Pi32(t)	8.65	C449

^aSNPs identified as having a significant permutation P -value (P < 0.01) detected by genome-wide association mapping in a high-yielding rice population. The SNPs chosen for testing represent frequently introgressed regions from japonica or indica parental cultivars.
^bQTL ID from Q-TARO database.