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 mr1246 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
vg0719011406 sf0719010413 7 19011406 1.69E-98 5.37E-26
vg0917780861 sf0917779860 9 17780861 4.82E-74 NA
vg0918588322 sf0918587321 9 18588322 5.58E-73 3.51E-07
vg0705232840 sf0705231841 7 5232840 3.31E-72 NA
vg0220874371 sf0220868503 2 20874371 5.40E-71 NA
vg0725752399 sf0725751405 7 25752399 6.57E-71 NA
vg0215798562 sf0215792692 2 15798562 2.03E-63 1.25E-06
vg0719091461 sf0719090468 7 19091461 NA 4.69E-22
vg0718955684 sf0718954691 7 18955684 NA 6.25E-13
vg0719071513 sf0719070520 7 19071513 NA 6.04E-12
vg0719045166 sf0719044173 7 19045166 NA 9.95E-12
vg0719087266 sf0719086273 7 19087266 NA 8.45E-11
vg0719140918 sf0719139925 7 19140918 NA 4.26E-10
vg0718886202 sf0718885209 7 18886202 NA 5.86E-10
vg0719346699 sf0719345706 7 19346699 NA 4.21E-09
vg0719466615 sf0719465622 7 19466615 NA 1.34E-07
vg0718996077 sf0718995084 7 18996077 NA 3.79E-07
vg0719432601 sf0719431608 7 19432601 NA 9.95E-07
vg0228211032 sf0228205163 2 28211032 NA 1.31E-06
vg1010998659 sf1010927479 10 10998659 NA 1.67E-06
vg0228211068 sf0228205199 2 28211068 NA 3.37E-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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