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 mr1917 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
vg0222887413 sf0222881544 2 22887413 1.03E-34 1.09E-14
vg0222673217 sf0222667348 2 22673217 1.37E-34 3.62E-16
vg0626309167 sf0626308170 6 26309167 8.60E-30 4.81E-06
vg0917445593 sf0917444592 9 17445593 2.02E-29 4.84E-06
vg0304690506 sf0304689508 3 4690506 7.39E-29 NA
vg0805989476 sf0805988479 8 5989476 1.16E-28 NA
vg1110591251 sf1110585796 11 10591251 2.38E-27 3.81E-08
vg0818212763 sf0818210050 8 18212763 2.68E-27 6.26E-07
vg0222734635 sf0222728766 2 22734635 3.10E-27 7.47E-08
vg0222738600 sf0222732731 2 22738600 1.04E-25 5.22E-07
vg0222952563 sf0222946694 2 22952563 NA 1.02E-08
vg0626215270 sf0626214273 6 26215270 NA 1.47E-08
vg0222722554 sf0222716685 2 22722554 NA 2.85E-08
vg1117963441 sf1117497299 11 17963441 NA 3.69E-08
vg1110033540 sf1110028117 11 10033540 NA 1.66E-07
vg0335906768 sf0335899637 3 35906768 NA 2.02E-07
vg0432750231 sf0432565117 4 32750231 NA 3.12E-07
vg1006914384 sf1006930007 10 6914384 NA 3.32E-07
vg0224158100 sf0224152231 2 24158100 NA 5.52E-07
vg0907026290 sf0907025290 9 7026290 NA 7.19E-07
vg0708623561 sf0708622566 7 8623561 NA 8.88E-07
vg0220854116 sf0220848248 2 20854116 NA 1.09E-06
vg1122328656 sf1121862527 11 22328656 NA 1.12E-06
vg0434789415 sf0434604306 4 34789415 NA 1.65E-06
vg0905697823 sf0905696823 9 5697823 NA 1.69E-06
vg0308157341 sf0308156279 3 8157341 NA 1.78E-06
vg1009556200 sf1009485021 10 9556200 NA 2.11E-06
vg0909362853 sf0909361852 9 9362853 NA 2.13E-06
vg1122364508 sf1121898379 11 22364508 NA 2.18E-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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