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 mr1036 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
vg0331249126 sf0331242011 3 31249126 4.28E-08 NA
vg0331261622 sf0331254507 3 31261622 8.66E-08 NA
vg0518299665 sf0518239151 5 18299665 1.42E-06 4.68E-06
vg0315672405 sf0315671052 3 15672405 NA 3.48E-06
vg1207352435 sf1207349842 12 7352435 NA 5.54E-06
vg0406708392 sf0406703839 4 6708392 NA 9.14E-06