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 mr1980 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
vg1013489724 sf1013418494 10 13489724 7.26E-30 1.64E-14
vg0418051899 sf0417879940 4 18051899 6.31E-16 4.01E-06
vg0825590083 sf0825587369 8 25590083 1.09E-14 NA
vg0817608868 sf0817606155 8 17608868 2.38E-14 4.46E-06
vg0821140572 sf0821137859 8 21140572 6.36E-14 NA
vg1121803238 sf1121337115 11 21803238 6.44E-13 7.00E-07
vg0718355901 sf0718354908 7 18355901 1.14E-09 1.30E-06
vg0718167360 sf0718166367 7 18167360 NA 1.93E-06
vg1221691088 sf1221657635 12 21691088 NA 3.37E-06