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 4.26E-108 6.85E-26
vg0917918788 sf0917917787 9 17918788 7.99E-89 NA
vg1201339510 sf1201338510 12 1339510 7.27E-85 NA
vg0708225849 sf0708224854 7 8225849 2.99E-84 NA
vg0305031973 sf0305030975 3 5031973 1.70E-83 1.64E-09
vg0719278912 sf0719277919 7 19278912 6.10E-82 2.23E-11
vg0917788203 sf0917787202 9 17788203 7.99E-81 8.45E-07
vg1201345845 sf1201344845 12 1345845 2.42E-80 8.27E-07
vg0719297467 sf0719296474 7 19297467 3.27E-78 1.60E-27
vg0707515285 sf0707514290 7 7515285 1.81E-77 1.38E-06
vg0719091461 sf0719090468 7 19091461 NA 1.93E-25
vg0718955684 sf0718954691 7 18955684 NA 6.10E-15
vg0719079053 sf0719078060 7 19079053 NA 1.19E-14
vg0719045166 sf0719044173 7 19045166 NA 6.91E-13
vg0719087589 sf0719086596 7 19087589 NA 4.72E-11
vg0718885795 sf0718884802 7 18885795 NA 1.57E-09
vg0719344789 sf0719343796 7 19344789 NA 2.78E-08
vg0718914481 sf0718913488 7 18914481 NA 7.03E-08
vg0719618102 sf0719617109 7 19618102 NA 1.27E-07
vg0726127290 sf0726126296 7 26127290 NA 2.54E-07
vg0718996077 sf0718995084 7 18996077 NA 6.76E-07
vg0718982411 sf0718981418 7 18982411 NA 8.93E-07
vg0722032999 sf0722032006 7 22032999 NA 1.08E-06
vg0719140779 sf0719139786 7 19140779 NA 1.19E-06
vg0719466615 sf0719465622 7 19466615 NA 1.64E-06
vg0719491368 sf0719490375 7 19491368 NA 2.00E-06
vg0714470500 sf0714469507 7 14470500 NA 3.13E-06
vg0718960800 sf0718959807 7 18960800 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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