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 mr1740 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
vg0500149447 sf0500149447 5 149447 1.70E-10 1.28E-07
vg0500152728 sf0500152728 5 152728 5.74E-10 1.06E-07
vg1215178307 sf1215175643 12 15178307 1.57E-08 8.34E-06
vg1121758646 sf1121292523 11 21758646 3.13E-08 NA
vg0229918162 sf0229912293 2 29918162 3.46E-08 NA
vg1105269119 sf1105264870 11 5269119 8.97E-08 5.68E-06
vg0103381628 sf0103380628 1 3381628 2.01E-06 NA
vg0121871143 sf0121870098 1 21871143 9.29E-06 NA