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 mr1733 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
vg0305026293 sf0305025295 3 5026293 6.62E-40 9.99E-06
vg0718741496 sf0718740503 7 18741496 2.12E-38 3.14E-07
vg0702568831 sf0702567832 7 2568831 1.93E-37 NA
vg0706960015 sf0706959020 7 6960015 2.41E-37 NA
vg0314943433 sf0314942080 3 14943433 2.66E-37 NA
vg0213987435 sf0213981565 2 13987435 3.99E-35 NA
vg0304752256 sf0304751258 3 4752256 4.34E-35 5.36E-06
vg0501517057 sf0501517041 5 1517057 NA 3.87E-07
vg0811826340 sf0811825345 8 11826340 NA 1.95E-06
vg1201903909 sf1201902907 12 1903909 NA 2.54E-06