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 mr1722 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
vg0231620487 sf0231614618 2 31620487 2.03E-10 2.79E-07
vg0232070505 sf0232064636 2 32070505 1.54E-09 1.59E-07
vg0904833561 sf0904832561 9 4833561 7.93E-09 NA
vg0801847604 sf0801846607 8 1847604 2.65E-08 NA
vg0210614424 sf0210614422 2 10614424 4.60E-08 NA
vg0725129140 sf0725128146 7 25129140 6.74E-08 NA
vg1209068690 sf1209066099 12 9068690 1.50E-07 1.04E-06
vg0904578294 sf0904577294 9 4578294 1.63E-06 NA
vg0406946931 sf0406942199 4 6946931 NA 9.73E-07
vg0129717613 sf0129716568 1 29717613 NA 1.24E-06
vg0900513558 sf0900512558 9 513558 NA 3.35E-06