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 mr1723 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
vg0333220949 sf0333213819 3 33220949 2.11E-52 2.79E-21
vg0330484032 sf0330476921 3 30484032 6.40E-35 NA
vg1225988493 sf1225954887 12 25988493 6.52E-34 NA
vg0335767848 sf0335760717 3 35767848 1.67E-33 NA
vg0231201837 sf0231195968 2 31201837 2.44E-33 NA
vg1225958017 sf1225924411 12 25958017 1.12E-32 1.35E-06
vg0333334135 sf0333327005 3 33334135 NA 1.22E-07
vg0332528512 sf0332521385 3 32528512 NA 2.11E-07
vg0333512165 sf0333505035 3 33512165 NA 4.27E-07
vg0409265113 sf0409260386 4 9265113 NA 2.68E-06
vg0808053956 sf0808052960 8 8053956 NA 2.68E-06
vg0910384464 sf0910383463 9 10384464 NA 4.61E-06