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 mr1435 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
vg0216822884 sf0216817014 2 16822884 7.17E-78 4.25E-34
vg0216562778 sf0216556908 2 16562778 4.46E-51 3.90E-10
vg0720349785 sf0720348792 7 20349785 3.03E-48 NA
vg0216735359 sf0216729489 2 16735359 7.19E-48 1.10E-10
vg0216898142 sf0216892272 2 16898142 3.06E-47 1.01E-10
vg0310327410 sf0310326326 3 10327410 1.19E-43 NA
vg1220844050 sf1220810599 12 20844050 1.77E-43 NA
vg0812023942 sf0812022947 8 12023942 1.52E-37 9.44E-12
vg0217137734 sf0217131864 2 17137734 NA 1.20E-17
vg0900337327 sf0900336327 9 337327 NA 8.65E-10
vg1005364262 sf1005380799 10 5364262 NA 5.26E-09
vg0213525745 sf0213525741 2 13525745 NA 5.27E-09
vg1114870126 sf1114406440 11 14870126 NA 8.35E-09
vg0216472199 sf0216466329 2 16472199 NA 1.02E-08
vg1114473442 sf1114009759 11 14473442 NA 2.05E-07
vg0404020437 sf0404016044 4 4020437 NA 4.40E-07
vg0216679265 sf0216673395 2 16679265 NA 5.24E-07
vg0217320352 sf0217314482 2 17320352 NA 7.24E-07
vg1112889066 sf1112425387 11 12889066 NA 7.54E-07
vg0404016698 sf0404012305 4 4016698 NA 8.14E-07
vg0216622303 sf0216616433 2 16622303 NA 1.03E-06
vg1105771186 sf1105766938 11 5771186 NA 1.32E-06
vg0216616335 sf0216610465 2 16616335 NA 1.35E-06
vg0804837959 sf0804836962 8 4837959 NA 1.53E-06
vg0216773376 sf0216767506 2 16773376 NA 2.59E-06
vg0618322026 sf0618321029 6 18322026 NA 3.66E-06
vg0720103372 sf0720102379 7 20103372 NA 4.51E-06