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 mr1682 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
vg0917565197 sf0917564196 9 17565197 6.83E-42 NA
vg0914739778 sf0914738777 9 14739778 1.90E-40 NA
vg0922500124 sf0922499643 9 22500124 3.27E-40 NA
vg0626081466 sf0626080469 6 26081466 4.63E-40 NA
vg1014200487 sf1014129253 10 14200487 1.00E-39 NA
vg1115099731 sf1114636045 11 15099731 1.36E-35 NA
vg0705702782 sf0705701783 7 5702782 NA 2.29E-09
vg1208638516 sf1208635923 12 8638516 NA 2.12E-07
vg0922324460 sf0922323979 9 22324460 NA 2.80E-07
vg1113156611 sf1112692932 11 13156611 NA 3.72E-07
vg1218022439 sf1217993875 12 18022439 NA 5.77E-07
vg0335630368 sf0335623237 3 35630368 NA 7.53E-07
vg1021514492 sf1021442969 10 21514492 NA 1.07E-06
vg0613699047 sf0613698048 6 13699047 NA 1.12E-06
vg0410038851 sf0410029548 4 10038851 NA 1.25E-06
vg0220953380 sf0220947512 2 20953380 NA 1.43E-06
vg0904461223 sf0904460223 9 4461223 NA 1.49E-06
vg0601213669 sf0601212670 6 1213669 NA 1.99E-06
vg0317255027 sf0317253837 3 17255027 NA 2.42E-06
vg0905240849 sf0905239849 9 5240849 NA 3.22E-06
vg0716748284 sf0716747291 7 16748284 NA 3.41E-06
vg0523768940 sf0523706361 5 23768940 NA 3.48E-06
vg0327530071 sf0327523124 3 27530071 NA 3.78E-06
vg0101342775 sf0101341775 1 1342775 NA 3.98E-06
vg1209066521 sf1209063930 12 9066521 NA 4.22E-06
vg0226125510 sf0226119641 2 26125510 NA 4.39E-06
vg1021514488 sf1021442965 10 21514488 NA 5.63E-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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