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 mr1023 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
vg1215869969 sf1215867265 12 15869969 2.53E-41 8.44E-19
vg1211776048 sf1211773384 12 11776048 3.11E-17 NA
vg0218184979 sf0218179110 2 18184979 2.86E-15 NA
vg0724571945 sf0724570951 7 24571945 2.97E-15 NA
vg0228693616 sf0228687747 2 28693616 1.15E-14 NA
vg0901048761 sf0901047761 9 1048761 NA 1.17E-07
vg1215870946 sf1215868242 12 15870946 NA 1.22E-07
vg1215915060 sf1215912356 12 15915060 NA 2.96E-07
vg1022588644 sf1022517118 10 22588644 NA 4.34E-07
vg1218663003 sf1218634438 12 18663003 NA 1.27E-06
vg0218132013 sf0218126144 2 18132013 NA 2.33E-06
vg0317414701 sf0317413511 3 17414701 NA 2.68E-06
vg0102116003 sf0102115003 1 2116003 NA 2.71E-06
vg0904368564 sf0904367564 9 4368564 NA 3.61E-06
vg1218152575 sf1218124011 12 18152575 NA 4.50E-06
vg1018579412 sf1018507969 10 18579412 NA 4.68E-06