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 mr1987 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
vg0215052036 sf0215046166 2 15052036 5.93E-125 3.59E-10
vg0321280227 sf0321278737 3 21280227 1.88E-124 1.52E-09
vg0321287375 sf0321285885 3 21287375 3.82E-124 3.13E-10
vg0317721273 sf0317720055 3 17721273 9.61E-123 1.12E-08
vg0317750910 sf0317749692 3 17750910 2.07E-119 1.01E-08
vg0313856271 sf0313854988 3 13856271 6.66E-116 9.43E-07
vg0327028819 sf0327021872 3 27028819 1.80E-115 NA
vg0917797570 sf0917796569 9 17797570 1.87E-115 2.38E-07
vg0914766218 sf0914765217 9 14766218 2.25E-113 4.44E-06
vg0212524956 sf0212524952 2 12524956 4.87E-112 2.00E-06
vg0111834681 sf0111833655 1 11834681 1.51E-102 1.36E-06
vg1218760084 sf1218731519 12 18760084 NA 1.76E-07
vg0815172680 sf0815169966 8 15172680 NA 6.15E-07
vg0208620450 sf0208620449 2 8620450 NA 7.65E-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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