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 mr1531 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
vg0608142371 sf0608141372 6 8142371 3.52E-29 2.05E-07
vg0608164173 sf0608163174 6 8164173 1.16E-26 1.06E-07
vg0230936995 sf0230931126 2 30936995 2.89E-26 NA
vg0142684702 sf0142683658 1 42684702 8.54E-26 NA
vg0507191831 sf0507191773 5 7191831 1.90E-25 6.33E-09
vg0611142895 sf0611141896 6 11142895 8.84E-25 NA
vg0728428950 sf0728427958 7 28428950 5.31E-21 2.36E-06
vg0304752208 sf0304751210 3 4752208 2.60E-20 2.84E-07
vg0507139485 sf0507139427 5 7139485 NA 1.20E-09
vg0507148577 sf0507148519 5 7148577 NA 1.25E-09
vg0507223574 sf0507223516 5 7223574 NA 1.75E-07
vg0304757375 sf0304756377 3 4757375 NA 4.79E-07
vg0721354156 sf0721353163 7 21354156 NA 8.48E-07
vg0223736839 sf0223730970 2 23736839 NA 3.17E-06
vg0608071095 sf0608070096 6 8071095 NA 4.27E-06
vg0230368237 sf0230362368 2 30368237 NA 6.29E-06
vg0805135920 sf0805134923 8 5135920 NA 7.74E-06