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 mr1103 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
vg0719011406 sf0719010413 7 19011406 1.35E-35 4.65E-28
vg0719007567 sf0719006574 7 19007567 1.76E-35 3.87E-26
vg1201654412 sf1201653412 12 1654412 2.45E-18 5.83E-08
vg0720355169 sf0720354176 7 20355169 3.51E-17 8.83E-09
vg0719242112 sf0719241119 7 19242112 4.23E-17 2.52E-10
vg0707730073 sf0707729078 7 7730073 6.66E-17 2.19E-06
vg1201345845 sf1201344845 12 1345845 2.97E-16 4.19E-08
vg0718998483 sf0718997490 7 18998483 NA 5.50E-17
vg0718985745 sf0718984752 7 18985745 NA 5.17E-11
vg0717307768 sf0717306775 7 17307768 NA 6.76E-09
vg0707515285 sf0707514290 7 7515285 NA 4.22E-08
vg0305009028 sf0305008030 3 5009028 NA 1.07E-07
vg0305031973 sf0305030975 3 5031973 NA 1.31E-07
vg0719459563 sf0719458570 7 19459563 NA 3.48E-07
vg0718885795 sf0718884802 7 18885795 NA 3.60E-07
vg0228211458 sf0228205589 2 28211458 NA 1.30E-06
vg0719143007 sf0719142014 7 19143007 NA 1.98E-06
vg0412911460 sf0412902168 4 12911460 NA 2.69E-06
vg0706750438 sf0706749443 7 6750438 NA 3.60E-06
vg0611538131 sf0611537132 6 11538131 NA 3.71E-06
vg0503738341 sf0503738318 5 3738341 NA 3.75E-06
vg0719140875 sf0719139882 7 19140875 NA 4.21E-06
vg1216280969 sf1216278265 12 16280969 NA 4.35E-06
vg0335349500 sf0335342369 3 35349500 NA 6.35E-06