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 mr1329 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
vg0321576069 sf0321574579 3 21576069 1.07E-08 1.07E-08
vg0222337580 sf0222331711 2 22337580 3.02E-08 3.02E-08
vg0901536604 sf0901535604 9 1536604 2.38E-07 2.38E-07
vg1125042488 sf1124576328 11 25042488 1.61E-06 1.61E-06
vg0610852582 sf0610851583 6 10852582 2.71E-06 2.71E-06
vg0826077942 sf0826075228 8 26077942 3.76E-06 3.76E-06
vg0807752750 sf0807751754 8 7752750 4.90E-06 4.90E-06