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 mr1841 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
vg1124335549 sf1123869393 11 24335549 1.97E-16 1.72E-13
vg0812486826 sf0812485730 8 12486826 6.55E-15 3.88E-11
vg0620312022 sf0620311025 6 20312022 9.52E-13 3.00E-08
vg1124965681 sf1124499521 11 24965681 1.74E-12 2.12E-12
vg0713136981 sf0713135988 7 13136981 4.85E-11 1.42E-07
vg0407782510 sf0407777778 4 7782510 7.88E-11 3.27E-07
vg0805901665 sf0805900668 8 5901665 9.29E-11 3.58E-07
vg0113026938 sf0113025912 1 13026938 1.80E-10 2.73E-08
vg1104422127 sf1104418029 11 4422127 3.20E-10 1.87E-08
vg0410375848 sf0410366547 4 10375848 3.45E-10 9.28E-07
vg0815665575 sf0815662861 8 15665575 2.05E-09 3.83E-07
vg0525249866 sf0525187287 5 25249866 2.88E-09 1.80E-06
vg1125316910 sf1124850750 11 25316910 1.49E-08 2.00E-07
vg0301969630 sf0301968626 3 1969630 1.55E-08 4.26E-06
vg0601001133 sf0601000134 6 1001133 2.38E-08 1.95E-07
vg0521578860 sf0521511524 5 21578860 3.28E-08 1.02E-06
vg1126219428 sf1125747842 11 26219428 2.69E-07 1.56E-06
vg0921997124 sf0921996643 9 21997124 5.00E-07 2.60E-06
vg0520747897 sf0520685338 5 20747897 6.15E-07 6.25E-07
vg0715539794 sf0715538801 7 15539794 7.68E-07 8.89E-08

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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