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Table 4 Top highest genome-wide significant association signals of agronomic traits using EMMAX

From: Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

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