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
vg0222746050 sf0222740181 2 22746050 2.00E-41 3.33E-23
vg0602873086 sf0602872087 6 2873086 3.67E-19 NA
vg0327464410 sf0327457463 3 27464410 6.98E-19 NA
vg0626585095 sf0626584098 6 26585095 2.73E-18 NA
vg0525138543 sf0525075964 5 25138543 3.45E-18 NA
vg0315944031 sf0315942678 3 15944031 1.55E-16 NA
vg0222725003 sf0222719134 2 22725003 NA 4.53E-13
vg0222634177 sf0222628308 2 22634177 NA 6.86E-08
vg0224876386 sf0224870517 2 24876386 NA 6.06E-07
vg0224640486 sf0224634617 2 24640486 NA 1.57E-06
vg0223506504 sf0223500635 2 23506504 NA 2.13E-06
vg0224830269 sf0224824400 2 24830269 NA 2.86E-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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