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 mr1320 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
vg0119923264 sf0119922219 1 19923264 6.98E-08 NA
vg0914981429 sf0914980428 9 14981429 9.82E-08 NA
vg0334659359 sf0334652229 3 34659359 NA 1.58E-06
vg0702446282 sf0702445283 7 2446282 NA 4.63E-06
vg0139005555 sf0139004512 1 39005555 NA 8.39E-06