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 mr1754 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
vg1211008261 sf1211005627 12 11008261 8.73E-08 3.53E-06
vg0825816468 sf0825813754 8 25816468 1.99E-07 2.41E-06
vg0500831203 sf0500831185 5 831203 2.73E-07 4.80E-06
vg0501809181 sf0501809164 5 1809181 2.74E-07 9.71E-07
vg0501795080 sf0501795063 5 1795080 1.39E-06 NA
vg0800828687 sf0800827689 8 828687 4.16E-06 NA
vg0407736903 sf0407732170 4 7736903 4.60E-06 3.75E-06
vg0907175535 sf0907174535 9 7175535 6.42E-06 9.93E-07
vg0400079399 sf0400078399 4 79399 8.82E-06 4.32E-06
vg0424185662 sf0424000523 4 24185662 NA 7.99E-07
vg0907667465 sf0907666465 9 7667465 NA 2.36E-06
vg1121614615 sf1121148492 11 21614615 NA 2.63E-06
vg0608003500 sf0608002501 6 8003500 NA 3.35E-06