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 mr1543 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
vg0221924055 sf0221918186 2 21924055 3.11E-14 2.60E-08
vg0221812870 sf0221807001 2 21812870 4.96E-14 1.90E-09
vg0221919301 sf0221913432 2 21919301 6.59E-14 2.06E-08
vg1217570924 sf1217564879 12 17570924 1.05E-13 NA
vg1115275633 sf1114811947 11 15275633 2.34E-13 NA
vg0824564743 sf0824562029 8 24564743 5.38E-13 NA
vg0128510736 sf0128509691 1 28510736 8.37E-12 2.70E-06
vg0212037119 sf0212037115 2 12037119 3.94E-11 2.85E-06
vg1216593584 sf1216590877 12 16593584 2.02E-10 NA
vg0113669976 sf0113668950 1 13669976 5.08E-10 6.30E-08