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 mr1740 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
vg0500154182 sf0500154182 5 154182 1.19E-10 2.35E-06
vg0432446609 sf0432261501 4 32446609 1.50E-10 2.35E-06
vg0920162302 sf0920161821 9 20162302 2.40E-10 NA
vg0909288154 sf0909287153 9 9288154 5.12E-10 NA
vg0810665700 sf0810664704 8 10665700 9.30E-10 NA
vg0432523918 sf0432338810 4 32523918 1.14E-09 1.20E-06
vg0432427528 sf0432242419 4 32427528 2.24E-09 1.60E-06
vg0919040682 sf0919040271 9 19040682 4.30E-07 NA
vg0500171547 sf0500171547 5 171547 7.08E-07 2.53E-07
vg1215178307 sf1215175643 12 15178307 2.00E-06 NA
vg0528836237 sf0528773592 5 28836237 5.48E-06 6.35E-07
vg1214656787 sf1214654127 12 14656787 NA 5.10E-08
vg1120477715 sf1120011640 11 20477715 NA 2.63E-06
vg0400387850 sf0400386848 4 387850 NA 4.73E-06