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 mr1709 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
vg1003467337 sf1003466314 10 3467337 7.17E-36 2.90E-16
vg1007541247 sf1007556859 10 7541247 1.14E-14 NA
vg0521310082 sf0521247523 5 21310082 8.99E-14 NA
vg1203610578 sf1203609577 12 3610578 1.46E-13 NA
vg1010151674 sf1010080495 10 10151674 2.90E-13 NA
vg0112848780 sf0112847754 1 12848780 5.60E-08 NA