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 mr1745 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
vg0430606062 sf0430420937 4 30606062 9.38E-70 7.20E-54
vg0430559445 sf0430374320 4 30559445 1.89E-69 1.79E-58
vg0430645227 sf0430460102 4 30645227 6.72E-53 1.46E-19
vg0430641254 sf0430456129 4 30641254 1.45E-52 4.41E-19
vg0921373579 sf0921373098 9 21373579 5.79E-49 NA
vg0128937112 sf0128936067 1 28937112 2.76E-48 NA
vg0605507888 sf0605506889 6 5507888 9.26E-47 NA
vg0430479634 sf0430294512 4 30479634 NA 7.33E-26
vg0430617232 sf0430432107 4 30617232 NA 3.83E-22
vg0430855895 sf0430670775 4 30855895 NA 2.84E-20
vg0430538279 sf0430353154 4 30538279 NA 1.28E-11
vg0307590023 sf0307588961 3 7590023 NA 1.31E-11
vg0225876283 sf0225870414 2 25876283 NA 2.46E-10
vg0430611308 sf0430426183 4 30611308 NA 2.71E-10
vg0919877661 sf0919877180 9 19877661 NA 4.86E-10
vg0430452456 sf0430267333 4 30452456 NA 6.50E-10
vg0325946462 sf0325944478 3 25946462 NA 1.96E-09
vg0124633522 sf0124632478 1 24633522 NA 2.04E-09
vg0221812870 sf0221807001 2 21812870 NA 3.34E-09
vg1125263510 sf1124797350 11 25263510 NA 3.75E-09
vg0307650234 sf0307649172 3 7650234 NA 1.10E-08
vg1125419173 sf1124953012 11 25419173 NA 1.55E-08
vg0216537545 sf0216531675 2 16537545 NA 1.91E-08
vg0430293825 sf0430108697 4 30293825 NA 2.11E-08
vg0617762306 sf0617761309 6 17762306 NA 2.33E-08
vg0519461555 sf0519399039 5 19461555 NA 2.79E-08
vg0802567454 sf0802566457 8 2567454 NA 3.53E-08
vg0325243401 sf0325241482 3 25243401 NA 4.37E-08
vg0701099543 sf0701098543 7 1099543 NA 4.39E-08
vg1015968448 sf1015897219 10 15968448 NA 9.85E-08
vg1121984717 sf1121518588 11 21984717 NA 1.15E-07
vg1122064371 sf1121598242 11 22064371 NA 3.03E-07
vg1100882780 sf1100881781 11 882780 NA 3.99E-07

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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