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 |