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 mr1734 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
vg0331781410 sf0331774287 3 31781410 7.32E-09 NA
vg0605723671 sf0605722672 6 5723671 8.18E-09 NA
vg0909136644 sf0909135643 9 9136644 3.18E-08 NA
vg0410973424 sf0410964125 4 10973424 6.98E-08 NA
vg0815655974 sf0815653260 8 15655974 8.49E-08 NA
vg0729303197 sf0729302205 7 29303197 6.61E-07 NA
vg0827076816 sf0827074102 8 27076816 4.61E-06 NA
vg1106169421 sf1106165173 11 6169421 NA 2.12E-06
vg0727614840 sf0727613846 7 27614840 NA 2.21E-06