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 mr1501 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
vg1215178307 sf1215175643 12 15178307 5.13E-07 5.13E-07
vg1104990849 sf1104986660 11 4990849 1.34E-06 1.34E-06
vg0816790944 sf0816788230 8 16790944 3.04E-06 3.04E-06
vg0914985761 sf0914984760 9 14985761 3.50E-06 3.50E-06
vg0130452108 sf0130451064 1 30452108 3.71E-06 3.71E-06
vg0431614108 sf0431429003 4 31614108 4.08E-06 4.08E-06