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 mr1037 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
vg0402389835 sf0402385430 4 2389835 9.40E-45 1.56E-13
vg0205658378 sf0205658378 2 5658378 1.20E-39 2.68E-07
vg1204503516 sf1204502504 12 4503516 7.60E-38 NA
vg0522015078 sf0521952520 5 22015078 4.64E-36 NA
vg0233990252 sf0233984383 2 33990252 4.77E-35 NA
vg0402373652 sf0402369247 4 2373652 NA 1.33E-08
vg1223626565 sf1223593021 12 23626565 NA 3.11E-07
vg0402308314 sf0402303909 4 2308314 NA 5.12E-07
vg0402386328 sf0402381923 4 2386328 NA 5.96E-07
vg0404609763 sf0404605366 4 4609763 NA 6.09E-07
vg0401972146 sf0401967742 4 1972146 NA 6.87E-07
vg1002324925 sf1002323902 10 2324925 NA 9.85E-07
vg0620427074 sf0620426077 6 20427074 NA 9.97E-07
vg0619650681 sf0619649684 6 19650681 NA 1.06E-06
vg0205660004 sf0205660004 2 5660004 NA 1.08E-06
vg0921454670 sf0921454189 9 21454670 NA 1.49E-06
vg1105648980 sf1105644732 11 5648980 NA 2.56E-06
vg0205657255 sf0205657255 2 5657255 NA 2.62E-06
vg0621705466 sf0621704469 6 21705466 NA 3.08E-06
vg0620431139 sf0620430142 6 20431139 NA 4.03E-06
vg1221482388 sf1221448935 12 21482388 NA 7.38E-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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