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 mr1705 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
vg0716393936 sf0716392943 7 16393936 9.33E-11 2.79E-06
vg1216364096 sf1216361392 12 16364096 2.16E-10 6.47E-07
vg0630178255 sf0630177257 6 30178255 1.98E-09 NA
vg0216568221 sf0216562351 2 16568221 5.03E-09 NA
vg0826521276 sf0826518562 8 26521276 6.45E-09 NA
vg1011259905 sf1011188725 10 11259905 9.33E-09 3.73E-06
vg0524686199 sf0524623619 5 24686199 9.58E-08 3.17E-07
vg0901718260 sf0901717260 9 1718260 NA 2.11E-06
vg0502285091 sf0502285066 5 2285091 NA 3.37E-06
vg0909394181 sf0909393180 9 9394181 NA 3.49E-06