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
vg1128511488 sf1127988267 11 28511488 2.02E-08 4.56E-06
vg0818521526 sf0818518813 8 18521526 2.38E-08 3.27E-06
vg1212211715 sf1212209053 12 12211715 6.21E-08 NA
vg1214008434 sf1214005774 12 14008434 8.73E-08 2.53E-06
vg1216247174 sf1216244470 12 16247174 9.92E-08 NA
vg1114908775 sf1114445089 11 14908775 2.44E-06 7.90E-06