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 mr1101 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
vg0222743508 sf0222737639 2 22743508 2.07E-58 1.01E-37
vg0222724011 sf0222718142 2 22724011 2.32E-58 1.47E-38
vg0906971590 sf0906970590 9 6971590 2.61E-39 3.76E-06
vg0222679274 sf0222673405 2 22679274 1.17E-38 2.33E-11
vg0222897061 sf0222891192 2 22897061 2.48E-37 7.05E-12
vg0702442806 sf0702441807 7 2442806 4.39E-36 NA
vg0529002068 sf0528939423 5 29002068 2.91E-35 NA
vg0721347769 sf0721346776 7 21347769 2.19E-34 2.52E-06
vg0624076189 sf0624075192 6 24076189 3.36E-29 2.04E-06
vg0907026290 sf0907025290 9 7026290 2.85E-27 1.33E-06
vg0434789415 sf0434604306 4 34789415 2.83E-26 5.54E-07
vg0222726952 sf0222721083 2 22726952 NA 9.68E-16
vg0222725003 sf0222719134 2 22725003 NA 4.86E-15
vg0224552398 sf0224546529 2 24552398 NA 3.54E-10
vg0224832469 sf0224826600 2 24832469 NA 1.81E-09
vg0222623646 sf0222617777 2 22623646 NA 1.40E-08
vg0218580570 sf0218574701 2 18580570 NA 5.05E-08
vg0222681985 sf0222676116 2 22681985 NA 2.35E-07
vg0222558409 sf0222552540 2 22558409 NA 5.87E-07
vg0222398309 sf0222392440 2 22398309 NA 7.52E-07
vg0222266766 sf0222260897 2 22266766 NA 8.87E-07
vg0224791280 sf0224785411 2 24791280 NA 9.61E-07
vg0232358383 sf0232352514 2 32358383 NA 9.89E-07
vg0523229276 sf0523166697 5 23229276 NA 1.19E-06
vg0222121191 sf0222115322 2 22121191 NA 1.52E-06
vg0224848674 sf0224842805 2 24848674 NA 2.00E-06
vg0222672641 sf0222666772 2 22672641 NA 2.22E-06
vg0525239875 sf0525177296 5 25239875 NA 2.65E-06
vg0232342588 sf0232336719 2 32342588 NA 5.02E-06