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 mr1080 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
vg0406465683 sf0406461126 4 6465683 2.33E-23 2.54E-17
vg0817327521 sf0817324807 8 17327521 9.31E-12 8.54E-08
vg1016522376 sf1016451149 10 16522376 5.71E-11 NA
vg1016503494 sf1016432267 10 16503494 4.53E-10 NA
vg0807357132 sf0807356137 8 7357132 1.55E-09 5.07E-07
vg0912864929 sf0912863928 9 12864929 1.66E-09 8.48E-07
vg0503312521 sf0503312497 5 3312521 5.03E-09 4.25E-06
vg0406056639 sf0406052078 4 6056639 1.11E-08 4.60E-08
vg1209797289 sf1209794699 12 9797289 4.03E-08 8.54E-07
vg1216561117 sf1216558410 12 16561117 4.88E-07 5.96E-07
vg1116610872 sf1116145750 11 16610872 2.40E-06 5.20E-07