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 mr1070 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
vg0135794714 sf0135793671 1 35794714 2.23E-18 8.79E-06
vg0130655033 sf0130653989 1 30655033 2.57E-16 NA
vg0910312862 sf0910311861 9 10312862 2.07E-15 1.20E-06
vg1203607472 sf1203606471 12 3607472 6.77E-15 NA
vg1122377333 sf1121911204 11 22377333 2.18E-14 NA
vg0907147216 sf0907146216 9 7147216 6.42E-14 3.68E-06
vg0130665696 sf0130664652 1 30665696 2.84E-12 NA
vg1009316722 sf1009245543 10 9316722 1.58E-10 1.24E-08
vg0130732040 sf0130730996 1 30732040 NA 7.36E-11
vg1009316724 sf1009245545 10 9316724 NA 1.30E-08
vg0907140771 sf0907139771 9 7140771 NA 1.59E-07
vg1009252761 sf1009181582 10 9252761 NA 7.01E-07
vg0134539333 sf0134538290 1 34539333 NA 1.05E-06
vg0412478616 sf0412469331 4 12478616 NA 1.51E-06
vg0311735208 sf0311733926 3 11735208 NA 1.56E-06
vg1010118163 sf1010046984 10 10118163 NA 2.36E-06
vg1122274012 sf1121807883 11 22274012 NA 3.01E-06
vg0120844010 sf0120842965 1 20844010 NA 4.70E-06
vg0821923639 sf0821920926 8 21923639 NA 5.74E-06