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
vg1214703763 sf1214701104 12 14703763 8.02E-08 NA
vg0618214950 sf0618213953 6 18214950 8.32E-08 NA
vg0317273290 sf0317272100 3 17273290 9.79E-08 NA
vg0316516166 sf0316514811 3 16516166 2.07E-06 5.17E-06
vg0316504158 sf0316502803 3 16504158 2.11E-06 3.34E-06
vg0401274821 sf0401270371 4 1274821 9.87E-06 NA