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 mr1131 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
vg0218614751 sf0218608882 2 18614751 9.25E-08 9.25E-08
vg0431422103 sf0431237001 4 31422103 4.20E-07 4.20E-07
vg0507093492 sf0507093434 5 7093492 8.18E-07 8.19E-07
vg1216567539 sf1216564832 12 16567539 1.40E-06 1.40E-06
vg0703303192 sf0703302193 7 3303192 3.72E-06 3.72E-06
vg1212214384 sf1212211722 12 12214384 4.33E-06 4.33E-06