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 mr1508 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
vg1206771466 sf1206770356 12 6771466 1.66E-08 NA
vg1103068554 sf1103064458 11 3068554 4.50E-08 NA
vg1126312813 sf1125841226 11 26312813 5.23E-08 NA
vg0904129442 sf0904128442 9 4129442 9.93E-08 NA
vg0504496687 sf0504496664 5 4496687 1.58E-07 4.83E-07
vg1103104667 sf1103100570 11 3104667 7.22E-07 NA
vg0800440463 sf0800439463 8 440463 7.41E-07 3.81E-06
vg0904232954 sf0904231954 9 4232954 7.45E-07 NA
vg0716255070 sf0716254077 7 16255070 NA 4.51E-06
vg0708117804 sf0708116809 7 8117804 NA 5.21E-06
vg0701901151 sf0701900152 7 1901151 NA 6.69E-06