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 mr1700 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
vg0910768444 sf0910767443 9 10768444 1.61E-07 1.61E-07
vg1126876944 sf1126405331 11 26876944 9.45E-07 9.45E-07
vg1128917038 sf1128393817 11 28917038 1.22E-06 1.22E-06
vg0402100710 sf0402096304 4 2100710 1.33E-06 1.33E-06
vg0217652051 sf0217646181 2 17652051 1.93E-06 1.93E-06
vg0140501355 sf0140500312 1 40501355 2.47E-06 2.47E-06
vg1114873399 sf1114409713 11 14873399 3.91E-06 3.92E-06
vg0406862618 sf0406858063 4 6862618 4.27E-06 4.27E-06