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 mr1038 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
vg0728442720 sf0728441728 7 28442720 1.30E-27 2.79E-18
vg1222591917 sf1222558356 12 22591917 2.36E-19 1.70E-12
vg0330077379 sf0330070418 3 30077379 2.02E-17 2.59E-09
vg0631155509 sf0631154511 6 31155509 3.30E-17 4.83E-08
vg0202925463 sf0202925461 2 2925463 7.80E-17 9.29E-12
vg0330452376 sf0330445265 3 30452376 3.45E-16 1.45E-09
vg0728693760 sf0728692768 7 28693760 1.05E-15 1.23E-11
vg0728665353 sf0728664361 7 28665353 9.12E-15 9.01E-08
vg0325722534 sf0325720552 3 25722534 2.82E-14 1.11E-08
vg0622846135 sf0622845138 6 22846135 7.45E-13 2.46E-08
vg1223831003 sf1223797456 12 23831003 1.20E-12 1.36E-07
vg1219448842 sf1219420312 12 19448842 1.33E-12 3.45E-09
vg0525542986 sf0525480407 5 25542986 1.63E-12 2.40E-07
vg0526514954 sf0526452318 5 26514954 2.46E-12 2.06E-09
vg0806359100 sf0806358105 8 6359100 1.09E-11 3.80E-08
vg0219929533 sf0219923665 2 19929533 1.41E-11 6.63E-08
vg1217972644 sf1217944080 12 17972644 2.50E-11 2.92E-08
vg0724944841 sf0724943847 7 24944841 5.30E-11 1.03E-07
vg1206967731 sf1206966621 12 6967731 5.85E-11 7.58E-08
vg1017360881 sf1017289654 10 17360881 2.21E-10 2.87E-06
vg1100433021 sf1100432024 11 433021 3.73E-09 6.72E-08
vg0406740172 sf0406735618 4 6740172 3.97E-08 9.36E-08
vg1019343930 sf1019272485 10 19343930 5.94E-06 NA
vg0526356726 sf0526294089 5 26356726 NA 1.48E-08
vg0800237681 sf0800236681 8 237681 NA 2.21E-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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