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 mr1456 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
vg0805546679 sf0805545682 8 5546679 2.72E-09 NA
vg0904941915 sf0904940915 9 4941915 2.99E-09 NA
vg0728454407 sf0728453415 7 28454407 1.08E-08 NA
vg0506230630 sf0506230569 5 6230630 1.28E-08 NA
vg0432282814 sf0432097706 4 32282814 1.57E-08 NA
vg0619684836 sf0619683839 6 19684836 2.37E-07 8.88E-07
vg1210023832 sf1210021243 12 10023832 5.94E-06 2.80E-08
vg0805616881 sf0805615884 8 5616881 NA 4.26E-07
vg0805068316 sf0805067319 8 5068316 NA 4.98E-07