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 mr1089 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
vg0216763637 sf0216757767 2 16763637 4.40E-20 3.15E-11
vg1219345800 sf1219317270 12 19345800 6.89E-15 5.35E-06
vg0520017792 sf0519955268 5 20017792 6.92E-15 NA
vg1216651011 sf1216644965 12 16651011 2.65E-14 4.36E-06
vg0132278599 sf0132277555 1 32278599 2.35E-13 NA
vg0130670983 sf0130669939 1 30670983 9.42E-11 2.76E-06
vg1011966171 sf1011894986 10 11966171 NA 9.45E-07
vg0418797097 sf0418625142 4 18797097 NA 2.16E-06
vg1203702115 sf1203701114 12 3702115 NA 3.30E-06