Table 4.

Top highest genome-wide significant association signals of agronomic traits using EMMAX

Trait	Significant loci	-log 10 (P)	genes	Genes position
Heading days	Chr1_40,209,752	4.56	OsMADS51	40,344,329~40,364,584
	Chr2_24,800,400	4.42	OSPRR1	24,569,294~24,572,560
	Chr3_1,342,491	4.59	DTH3	1,269,856~1,271,783
	Chr3_32,824,935	6.21	CKI	32,999,502~33,006,898
	Chr4_32,895,071	4.69	HAF1	33,022,716~33,028,387
	Chr6_9,156,215	4.78	Hd1	9,336,359~9,338,643
	Chr12_5,600,578	4.55	OsMADS13	5,586,131~5,590,285
Plant height	Chr1_38,483,533	4.85	SD1	38,382,382~38,385,504
	Chr7_9,235,801	4.38	Ghd7	9,152,402~9,155,185
	Chr8_4,056,392	4.70	Ghd8	4,333,717~4,335,434
Seed set rate	Chr1_6,369,510	5.15	SPP1	6,528,797~6,630,463
	Chr10_18,962,735	4.41	Rf-1	18,935,690~18,942,573
Panicle length	Chr1_29,750,254	4.39	OsBRI1	29,927,543~29,931,487
	Chr2_9,035,894	4.31	LP	9,042,076~9,046,141
	Chr3_10,779,794	4.69	SSD1	10,684,315~10,688,955
	Chr7_28,613,922	5.20	FZP	28,299,591~28,301,089
	Chr9_16,891,286	4.12	LP1	17,182,867~17,188,378
	Chr11_7,007,154	4.23	SP1	7,193,230~7,198,552
Grain length	Chr3_16,876,884	4.12	GS3	16,729,501~16,735,109
	Chr6_25,249,340	4.46	TGW6	25,093,242~25,094,294
Grain width	Chr2_8,073,466	4.28	GW2	8,114,961~8,121,925
	Chr2_28,875,239	4.33	GS2	28,863,173~28,866,997
	Chr3_17,360,192	4.45	GL3.2	17,340,415~17,342,284
	Chr5_3,576,630	4.45	GS5	3,439,259~3,443,769
	Chr6_1,281,784	5.07	GS6	1,465,499~1,468,600
	Chr6_25,355,332	4.62	TGW6	25,093,242~25,094,294
	Chr8_26,162,707	4.61	OsSPL16	26,501,167~26,506,218
	Chr8_28,114,414	4.44	SLG	28,162,970~28,165,431
100 grains weight	Chr5_5,539,341	3.73	GW5	5,365,122~5,366,701
	Chr6_25,216,303	4.01	TGW6	25,093,242~25,094,294
	Chr7_24,377,379	3,69	GL7	24,664,168~24,669,324
	Chr8_26,475,471	3.78	OsSPL16	26,501,167~26,506,218