Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1300 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1000443503 sf1000442479 10 443503 1.97E-50 9.05E-29
vg1125127481 sf1124661321 11 25127481 3.36E-29 4.23E-11
vg0528146502 sf0528083857 5 28146502 5.77E-29 1.01E-12
vg1010974418 sf1010903238 10 10974418 1.36E-27 1.34E-08
vg1008207053 sf1008135915 10 8207053 3.05E-27 7.12E-10
vg1008205459 sf1008134321 10 8205459 9.02E-27 4.49E-10
vg0202330989 sf0202330987 2 2330989 1.05E-25 5.78E-08
vg0402461396 sf0402456994 4 2461396 5.59E-22 1.51E-07
vg1125090609 sf1124624449 11 25090609 NA 5.00E-15
vg1125082353 sf1124616193 11 25082353 NA 3.10E-14
vg1125116259 sf1124650099 11 25116259 NA 7.24E-14
vg1001020266 sf1001019242 10 1020266 NA 8.82E-11
vg1004952643 sf1004969180 10 4952643 NA 4.14E-10
vg1000232970 sf1000231970 10 232970 NA 9.64E-08
vg0415096885 sf0415087600 4 15096885 NA 1.74E-07
vg0817400578 sf0817397864 8 17400578 NA 2.03E-07
vg0504190129 sf0504188922 5 4190129 NA 2.08E-07
vg1001512331 sf1001511308 10 1512331 NA 2.46E-07
vg1000958635 sf1000957611 10 958635 NA 2.61E-07
vg0528175919 sf0528113274 5 28175919 NA 2.80E-07
vg1219598626 sf1219570096 12 19598626 NA 3.13E-07
vg0109677594 sf0109676570 1 9677594 NA 3.13E-07
vg0803730363 sf0803729366 8 3730363 NA 3.51E-07
vg0330670598 sf0330663485 3 30670598 NA 4.25E-07
vg0129917055 sf0129916010 1 29917055 NA 4.36E-07
vg0307992391 sf0307991329 3 7992391 NA 5.01E-07