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 mr1509 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
vg1020493947 sf1020422426 10 20493947 2.67E-66 6.74E-15
vg1020420315 sf1020348794 10 20420315 2.81E-66 9.90E-16
vg0129959121 sf0129958076 1 29959121 8.99E-52 NA
vg0324070014 sf0324068093 3 24070014 6.01E-51 NA
vg0704675216 sf0704674217 7 4675216 1.68E-50 NA
vg0332643360 sf0332636231 3 32643360 2.45E-50 NA
vg0122331148 sf0122330103 1 22331148 NA 1.91E-07
vg0410227364 sf0410218061 4 10227364 NA 1.13E-06
vg0142242102 sf0142241058 1 42242102 NA 2.21E-06
vg0221436059 sf0221430191 2 21436059 NA 2.46E-06
vg0612813818 sf0612812819 6 12813818 NA 3.04E-06
vg1124474270 sf1124008110 11 24474270 NA 3.37E-06
vg1208765892 sf1208763299 12 8765892 NA 3.78E-06
vg1124474136 sf1124007976 11 24474136 NA 3.94E-06
vg0914907095 sf0914906094 9 14907095 NA 4.41E-06
vg0233244719 sf0233238850 2 33244719 NA 4.70E-06
vg0208558888 sf0208558887 2 8558888 NA 4.94E-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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