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 mr1222 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
vg0222745001 sf0222739132 2 22745001 1.39E-28 2.81E-20
vg0222746186 sf0222740317 2 22746186 1.68E-28 2.32E-20
vg0722959446 sf0722958453 7 22959446 9.43E-13 NA
vg0809946687 sf0809945691 8 9946687 2.76E-12 NA
vg0321480693 sf0321479203 3 21480693 1.42E-11 NA
vg0906131677 sf0906130677 9 6131677 3.54E-11 NA
vg0503366137 sf0503366114 5 3366137 1.77E-10 3.68E-06
vg0529272168 sf0529209523 5 29272168 2.42E-10 1.24E-06
vg0222634177 sf0222628308 2 22634177 3.49E-10 1.40E-06
vg0224832604 sf0224826735 2 24832604 1.56E-07 1.99E-06
vg0222567385 sf0222561516 2 22567385 NA 5.30E-08
vg0524973304 sf0524910719 5 24973304 NA 3.33E-07
vg0224822342 sf0224816473 2 24822342 NA 2.60E-06
vg0222729853 sf0222723984 2 22729853 NA 4.22E-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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