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 mr1099 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
vg0904766722 sf0904765722 9 4766722 3.43E-08 5.74E-06
vg0400034044 sf0400033044 4 34044 1.39E-06 3.52E-07
vg0727090466 sf0727089472 7 27090466 1.89E-06 9.77E-07
vg0221025908 sf0221020040 2 21025908 2.03E-06 2.23E-07
vg0702433302 sf0702432303 7 2433302 2.32E-06 1.00E-06
vg0222833455 sf0222827586 2 22833455 2.36E-06 8.20E-07
vg0919581492 sf0919581082 9 19581492 NA 1.80E-06
vg0728303039 sf0728302047 7 28303039 NA 2.38E-06
vg0901835907 sf0901834907 9 1835907 NA 4.98E-06