Phenotype and GWAS Information

Note: Select an agronomic trait and population to view its distribution and accession-level phenotype measurements.

Phenotype Search

Note: Select a trait, study and population to view association results. The six additional cohorts contain 315 reported peak-SNP records from RiceNavi Supplementary Dataset 3, rather than genome-wide summary statistics. Plots can therefore contain only one or a few points. The original Xie (2015) and Chen (2014) results retain their existing coverage and methods.

Agronomic Trait GWAS

Metabolic Trait GWAS

GWAS Results

Chen et al. 2014, Nat Genet — Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. A second replication ends with “_2”, for example “mr1002_2”.

Detailed information about mr1745 is available from the rice metabolite database.

Manhattan Plot

Results are retained when the LR or LMM P-value is ≤ 1e-5 or its rank is within the top 20,000. The plot shows LMM results.

Significant Candidate Loci (Lead Variant)

Variation ID Variation ID V6 Chromosome Position LR P-value LMM P-value
vg0430597974 sf0430412849 4 30597974 1.53E-59 1.70E-34
vg0430613365 sf0430428240 4 30613365 3.36E-59 7.60E-35
vg0128937112 sf0128936067 1 28937112 3.17E-41 NA
vg0430645227 sf0430460102 4 30645227 1.22E-39 8.85E-10
vg0921373579 sf0921373098 9 21373579 2.07E-39 NA
vg0310172690 sf0310171606 3 10172690 1.57E-37 NA
vg0430617159 sf0430432034 4 30617159 NA 3.98E-15
vg1125263510 sf1124797350 11 25263510 NA 7.87E-14
vg0430479763 sf0430294641 4 30479763 NA 1.60E-13
vg0429938561 sf0429753428 4 29938561 NA 4.92E-13
vg1125403382 sf1124937221 11 25403382 NA 2.65E-11
vg1125263117 sf1124796957 11 25263117 NA 2.17E-10
vg0430855895 sf0430670775 4 30855895 NA 4.13E-10
vg0430538279 sf0430353154 4 30538279 NA 1.44E-09
vg1015945404 sf1015874175 10 15945404 NA 2.29E-09
vg0225876283 sf0225870414 2 25876283 NA 3.60E-09
vg0919877661 sf0919877180 9 19877661 NA 5.07E-09
vg0331916551 sf0331909428 3 31916551 NA 1.04E-08
vg1125601372 sf1125135211 11 25601372 NA 1.24E-08
vg0307337230 sf0307336228 3 7337230 NA 1.26E-08
vg0204236567 sf0204236564 2 4236567 NA 1.36E-08
vg0325243401 sf0325241482 3 25243401 NA 1.49E-08
vg1015868542 sf1015797312 10 15868542 NA 1.82E-08
vg1128170551 sf1127647330 11 28170551 NA 2.85E-08
vg0432702205 sf0432517094 4 32702205 NA 5.81E-08
vg0324085319 sf0324083398 3 24085319 NA 9.81E-08
vg0433305431 sf0433120321 4 33305431 NA 1.27E-07
vg0518913277 sf0518850761 5 18913277 NA 1.36E-07

Information

This page provides two coordinated modules for trait exploration. Use Phenotype to inspect accession-level measurements and population distributions, or switch to GWAS Results to inspect association signals, Manhattan plots, and lead variants.

Keeping the two workflows on one page makes it possible to move between observed trait variation and its genetic associations without mixing their search controls or result tables.

GWAS results were collected from Xie et al. (2015) and Chen et al. (2014), with additional peak-SNP information obtained from RiceNavi and Wei et al. (2021). Specifically, we collected GWAS peak SNPs linked to functionally characterized rice genes from six populations or panels analyzed by Wei et al. (2021), including Chinese rice accessions (Li et al., 2020), Japanese rice accessions (Yano et al., 2016), the 3K rice panel (Wang et al., 2018), hybrid rice F1 populations (Huang et al., 2015), the QTN library (Wei et al., 2021), and RDP1 (Zhao et al., 2011).


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