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 mr1081 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
vg1203947894 sf1203946893 12 3947894 1.05E-36 NA
vg0915107312 sf0915106311 9 15107312 6.34E-36 NA
vg0230085254 sf0230079385 2 30085254 1.49E-35 NA
vg0721770705 sf0721769712 7 21770705 1.77E-35 NA
vg0118710442 sf0118709396 1 18710442 2.53E-35 NA
vg0222732157 sf0222726288 2 22732157 NA 1.10E-07
vg0421031231 sf0420859284 4 21031231 NA 3.03E-06
vg1203473350 sf1203472350 12 3473350 NA 3.91E-06
vg0102113150 sf0102112150 1 2113150 NA 4.08E-06