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 mr1708 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
vg0814903603 sf0814900889 8 14903603 6.02E-12 1.73E-09
vg0811898736 sf0811897741 8 11898736 4.79E-11 1.67E-07
vg0811929425 sf0811928430 8 11929425 5.95E-11 8.61E-08
vg1004841432 sf1004857969 10 4841432 9.22E-10 2.64E-08
vg0805115588 sf0805114591 8 5115588 5.84E-09 NA
vg1004482171 sf1004498709 10 4482171 1.47E-08 5.17E-07
vg0313149208 sf0313147926 3 13149208 1.67E-08 7.08E-06
vg1004835334 sf1004851871 10 4835334 9.43E-08 8.60E-07
vg0228934167 sf0228928298 2 28934167 2.35E-07 NA
vg1004618887 sf1004635425 10 4618887 2.72E-07 1.81E-07
vg1004582886 sf1004599424 10 4582886 NA 9.98E-07