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 mr1865 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
vg0922415213 sf0922414732 9 22415213 2.96E-102 1.21E-23
vg0922416727 sf0922416246 9 22416727 1.07E-93 8.04E-20
vg0922428117 sf0922427636 9 22428117 1.20E-87 3.76E-34
vg0916404897 sf0916403896 9 16404897 1.71E-80 NA
vg0304866487 sf0304865489 3 4866487 6.39E-78 NA
vg0309927258 sf0309926194 3 9927258 2.58E-77 NA
vg1203225321 sf1203224324 12 3225321 3.98E-76 NA
vg0717006246 sf0717005253 7 17006246 2.19E-71 2.66E-06
vg0613084325 sf0613083326 6 13084325 4.20E-69 7.90E-07
vg0922436617 sf0922436136 9 22436617 NA 6.97E-21
vg0922417122 sf0922416641 9 22417122 NA 3.17E-17
vg0922451431 sf0922450950 9 22451431 NA 9.42E-13
vg0922560785 sf0922560304 9 22560785 NA 1.51E-10
vg0922565216 sf0922564735 9 22565216 NA 1.35E-07
vg0922403934 sf0922403453 9 22403934 NA 1.73E-07
vg0922300827 sf0922300346 9 22300827 NA 2.01E-07
vg0904740928 sf0904739928 9 4740928 NA 2.70E-07
vg0922494091 sf0922493610 9 22494091 NA 2.71E-07
vg0912946767 sf0912945766 9 12946767 NA 2.43E-06
vg0330337817 sf0330330856 3 30337817 NA 3.72E-06
vg0922202326 sf0922201845 9 22202326 NA 4.29E-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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