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 mr1146 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
vg0222743526 sf0222737657 2 22743526 5.90E-51 1.01E-28
vg0222746050 sf0222740181 2 22746050 1.03E-50 3.77E-29
vg1207773391 sf1207770797 12 7773391 2.50E-21 NA
vg0722483807 sf0722482814 7 22483807 3.18E-21 NA
vg0406998246 sf0406993517 4 6998246 1.03E-20 NA
vg0713719162 sf0713718169 7 13719162 2.07E-20 NA
vg1215239496 sf1215236793 12 15239496 9.74E-19 3.36E-06
vg0220963033 sf0220957165 2 20963033 2.43E-17 NA
vg0125220764 sf0125219720 1 25220764 4.80E-17 NA
vg0222725003 sf0222719134 2 22725003 NA 2.62E-17
vg0222817468 sf0222811599 2 22817468 NA 4.85E-07
vg0524971409 sf0524908824 5 24971409 NA 9.92E-07
vg0224676560 sf0224670691 2 24676560 NA 1.10E-06
vg0222558409 sf0222552540 2 22558409 NA 1.47E-06
vg0525072434 sf0525009849 5 25072434 NA 1.89E-06
vg0433003871 sf0432818757 4 33003871 NA 3.88E-06
vg0222735022 sf0222729153 2 22735022 NA 4.39E-06
vg0211185461 sf0211185458 2 11185461 NA 6.14E-06

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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