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 mr1484 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
vg1125085416 sf1124619256 11 25085416 1.36E-10 3.54E-09
vg1124335549 sf1123869393 11 24335549 3.44E-10 3.67E-09
vg0815306355 sf0815303641 8 15306355 1.30E-09 2.83E-08
vg0314909213 sf0314907860 3 14909213 2.02E-08 3.11E-08
vg1125990989 sf1125519403 11 25990989 2.49E-08 3.18E-07
vg0815806693 sf0815803979 8 15806693 2.50E-08 2.94E-06
vg0814220352 sf0814217638 8 14220352 3.26E-08 6.79E-07
vg0815800560 sf0815797846 8 15800560 5.23E-08 7.59E-07
vg1104596397 sf1104592299 11 4596397 1.17E-07 9.27E-07
vg0715539794 sf0715538801 7 15539794 1.86E-07 4.96E-07
vg0811469683 sf0811468688 8 11469683 5.29E-07 1.84E-06
vg0811646982 sf0811645987 8 11646982 6.50E-07 3.99E-06
vg0526332116 sf0526269479 5 26332116 7.33E-07 5.31E-07
vg0208128713 sf0208128712 2 8128713 9.28E-07 1.98E-06
vg1214799098 sf1214796439 12 14799098 1.82E-06 2.69E-06
vg1124940229 sf1124474069 11 24940229 1.83E-06 2.55E-06
vg1214931700 sf1214929042 12 14931700 2.08E-06 1.67E-06
vg0526675403 sf0526612761 5 26675403 NA 2.47E-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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