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 mr1351 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
vg0305021978 sf0305020980 3 5021978 1.96E-08 NA
vg1123192315 sf1122726186 11 23192315 6.62E-08 NA
vg0910776286 sf0910775285 9 10776286 8.68E-08 NA
vg0220716138 sf0220710270 2 20716138 4.15E-07 NA
vg0701309447 sf0701308447 7 1309447 2.74E-06 NA
vg0426278854 sf0426093727 4 26278854 3.08E-06 5.13E-06
vg0712096394 sf0712095400 7 12096394 NA 4.78E-06