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 mr1540 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
vg1216303123 sf1216300419 12 16303123 3.29E-20 NA
vg0129891018 sf0129889973 1 29891018 9.35E-20 3.95E-06
vg0309337354 sf0309336290 3 9337354 1.64E-19 NA
vg1016081589 sf1016010361 10 16081589 1.69E-19 NA
vg1016228595 sf1016157367 10 16228595 1.87E-19 1.85E-06
vg1215474654 sf1215471951 12 15474654 2.33E-19 2.61E-06
vg0726879159 sf0726878165 7 26879159 5.91E-19 NA
vg0903780051 sf0903779051 9 3780051 5.61E-18 NA
vg0906778436 sf0906777436 9 6778436 NA 2.87E-06
vg0107647091 sf0107646091 1 7647091 NA 4.87E-06