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 mr1276 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
vg0232480149 sf0232474280 2 32480149 2.83E-24 4.58E-07
vg0621000813 sf0620999816 6 21000813 8.76E-24 2.88E-06
vg0306755393 sf0306754393 3 6755393 1.49E-22 NA
vg1018095995 sf1018024766 10 18095995 6.10E-22 NA
vg0611852180 sf0611851181 6 11852180 1.46E-21 NA
vg1012820139 sf1012748954 10 12820139 NA 9.24E-07
vg0224543759 sf0224537890 2 24543759 NA 1.03E-06
vg0718397736 sf0718396743 7 18397736 NA 2.93E-06