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 mr1580 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
vg1005802057 sf1005818595 10 5802057 8.58E-12 1.09E-06
vg1209796367 sf1209793777 12 9796367 4.26E-10 NA
vg0820461846 sf0820459133 8 20461846 1.29E-09 NA
vg0403275975 sf0403271578 4 3275975 5.70E-09 NA
vg0804780756 sf0804779759 8 4780756 6.52E-09 NA
vg0526324545 sf0526261908 5 26324545 1.58E-08 NA
vg1005758603 sf1005775141 10 5758603 3.70E-08 2.71E-06
vg1006051095 sf1006067633 10 6051095 3.80E-08 6.58E-07
vg1121128751 sf1120662630 11 21128751 4.17E-08 NA
vg0813652209 sf0813649494 8 13652209 2.28E-07 2.27E-06
vg1008973707 sf1008902568 10 8973707 5.85E-07 1.72E-06
vg0614828122 sf0614827123 6 14828122 5.37E-06 NA
vg0111338686 sf0111337662 1 11338686 NA 2.36E-06