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 mr1546 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
vg1209234365 sf1209231774 12 9234365 2.02E-22 3.10E-09
vg1212726422 sf1212723761 12 12726422 1.48E-20 3.41E-10
vg1209209246 sf1209206655 12 9209246 1.58E-20 4.81E-10
vg1215400087 sf1215397385 12 15400087 6.61E-20 2.92E-07
vg1215977007 sf1215974303 12 15977007 5.09E-19 1.70E-08
vg1223827289 sf1223793742 12 23827289 2.93E-18 NA
vg0526274314 sf0526211678 5 26274314 1.57E-16 NA
vg1223992204 sf1223958657 12 23992204 1.78E-15 2.78E-07