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 mr1108 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
vg0610566343 sf0610565344 6 10566343 5.09E-93 1.74E-27
vg0610459123 sf0610458124 6 10459123 6.43E-80 5.22E-24
vg0719209059 sf0719208066 7 19209059 2.92E-58 NA
vg0616950705 sf0616949708 6 16950705 2.23E-56 NA
vg0627273915 sf0627272918 6 27273915 6.28E-54 NA
vg0122402967 sf0122401922 1 22402967 1.46E-52 NA
vg0617383481 sf0617382484 6 17383481 3.51E-47 2.10E-07
vg0613066999 sf0613066000 6 13066999 2.43E-44 3.21E-07
vg0610763769 sf0610762770 6 10763769 NA 1.36E-11
vg0610776489 sf0610775490 6 10776489 NA 7.75E-09
vg0610393322 sf0610392323 6 10393322 NA 3.00E-08
vg0609930953 sf0609929954 6 9930953 NA 3.07E-08
vg0611127099 sf0611126100 6 11127099 NA 4.42E-08
vg0609902440 sf0609901441 6 9902440 NA 5.33E-08
vg0610014317 sf0610013318 6 10014317 NA 6.96E-08
vg0617631923 sf0617630926 6 17631923 NA 8.29E-08
vg0610061410 sf0610060411 6 10061410 NA 9.92E-08
vg0610707600 sf0610706601 6 10707600 NA 1.24E-07
vg0611990477 sf0611989478 6 11990477 NA 1.49E-07
vg0609975418 sf0609974419 6 9975418 NA 6.50E-07
vg0610674623 sf0610673624 6 10674623 NA 7.32E-07
vg0610444069 sf0610443070 6 10444069 NA 1.17E-06
vg0611818263 sf0611817264 6 11818263 NA 1.22E-06
vg0614543893 sf0614542894 6 14543893 NA 1.33E-06
vg1127845569 sf1127373955 11 27845569 NA 1.56E-06
vg0617641436 sf0617640439 6 17641436 NA 1.61E-06
vg1017131896 sf1017060668 10 17131896 NA 2.69E-06
vg1006914384 sf1006930007 10 6914384 NA 7.54E-06