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 mr1530 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
vg0430582450 sf0430397325 4 30582450 9.67E-32 3.90E-11
vg1125429805 sf1124963644 11 25429805 2.71E-24 2.64E-13
vg0707341833 sf0707340838 7 7341833 3.80E-23 NA
vg1225819892 sf1225786286 12 25819892 6.41E-23 NA
vg0124437276 sf0124436232 1 24437276 7.02E-23 NA
vg0430723225 sf0430538100 4 30723225 3.04E-19 4.46E-06
vg0206023772 sf0206023772 2 6023772 1.02E-18 8.40E-06
vg1125419173 sf1124953012 11 25419173 1.35E-15 9.24E-13
vg1125418435 sf1124952274 11 25418435 NA 2.41E-08
vg0430617282 sf0430432157 4 30617282 NA 5.48E-08
vg1125555777 sf1125089616 11 25555777 NA 7.04E-08
vg0204148254 sf0204148251 2 4148254 NA 2.27E-07
vg1000621991 sf1000620967 10 621991 NA 3.78E-07
vg0138012096 sf0138011053 1 38012096 NA 5.05E-07
vg0140474503 sf0140473460 1 40474503 NA 8.90E-07
vg0324638889 sf0324636968 3 24638889 NA 1.43E-06
vg1125280367 sf1124814207 11 25280367 NA 1.52E-06
vg0430820905 sf0430635782 4 30820905 NA 2.48E-06
vg0607207993 sf0607206994 6 7207993 NA 2.52E-06
vg0401597768 sf0401593317 4 1597768 NA 3.19E-06
vg0226677364 sf0226671495 2 26677364 NA 3.38E-06
vg0821271128 sf0821268415 8 21271128 NA 3.58E-06
vg1220880817 sf1220847366 12 20880817 NA 3.97E-06
vg0313149395 sf0313148113 3 13149395 NA 4.78E-06
vg0604683982 sf0604682983 6 4683982 NA 4.93E-06