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 mr1721 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
vg1001388777 sf1001387754 10 1388777 4.46E-12 3.70E-08
vg1001395945 sf1001394922 10 1395945 4.94E-12 3.11E-08
vg0720057946 sf0720056953 7 20057946 4.47E-08 NA
vg0724248659 sf0724247665 7 24248659 4.57E-06 NA
vg0806065496 sf0806064501 8 6065496 4.90E-06 4.18E-06
vg1005112746 sf1005129283 10 5112746 6.37E-06 2.01E-06
vg0701714318 sf0701713319 7 1714318 NA 4.67E-06