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 mr1301 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
vg1217441137 sf1217435092 12 17441137 1.25E-25 7.27E-10
vg1210452682 sf1210450095 12 10452682 4.18E-25 1.91E-08
vg1223873419 sf1223839872 12 23873419 1.09E-20 NA
vg1214919555 sf1214916897 12 14919555 3.13E-19 NA
vg0526318636 sf0526255999 5 26318636 9.95E-18 NA
vg1215678000 sf1215675297 12 15678000 NA 4.12E-07
vg0706567685 sf0706566690 7 6567685 NA 5.55E-07
vg0504497766 sf0504497743 5 4497766 NA 2.00E-06
vg0904153122 sf0904152122 9 4153122 NA 2.18E-06
vg0900074360 sf0900073360 9 74360 NA 2.55E-06
vg0304623015 sf0304622017 3 4623015 NA 4.05E-06
vg0919940257 sf0919939776 9 19940257 NA 4.29E-06
vg0315903149 sf0315901796 3 15903149 NA 4.35E-06
vg0820664167 sf0820661454 8 20664167 NA 4.63E-06
vg0311297778 sf0311296496 3 11297778 NA 4.81E-06