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 mr1105 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
vg0115333877 sf0115332851 1 15333877 3.97E-08 NA
vg0823456313 sf0823453600 8 23456313 2.01E-07 NA
vg1226213776 sf1226180170 12 26213776 2.32E-06 NA
vg0324081467 sf0324079546 3 24081467 7.41E-06 2.17E-06
vg0118433273 sf0118432227 1 18433273 9.30E-06 NA