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 mr1137 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
vg0604350087 sf0604349088 6 4350087 1.10E-73 2.11E-37
vg0604357002 sf0604356003 6 4357002 1.19E-73 2.05E-37
vg0207150816 sf0207150816 2 7150816 7.23E-45 4.19E-13
vg1021135316 sf1021063795 10 21135316 2.28E-40 6.07E-07
vg1224843226 sf1224809680 12 24843226 3.66E-40 7.22E-07
vg0313641931 sf0313640648 3 13641931 1.10E-37 7.77E-09
vg0910028393 sf0910027392 9 10028393 2.85E-37 4.45E-09
vg0912901940 sf0912900939 9 12901940 4.38E-37 2.65E-07
vg0128528170 sf0128527125 1 28528170 1.95E-35 8.00E-09
vg1000904661 sf1000903637 10 904661 3.78E-34 6.78E-08
vg0808821102 sf0808820106 8 8821102 6.79E-34 2.31E-07
vg0702730576 sf0702729577 7 2730576 8.56E-34 3.52E-08
vg1223038204 sf1223004664 12 23038204 5.75E-32 3.05E-09
vg0216502492 sf0216496622 2 16502492 1.10E-31 2.82E-07
vg1123325178 sf1122859048 11 23325178 1.11E-31 2.89E-08
vg0617571208 sf0617570211 6 17571208 1.09E-30 4.86E-08
vg0401281473 sf0401277023 4 1281473 1.66E-30 2.51E-09
vg1116506738 sf1116041615 11 16506738 2.40E-30 4.24E-09
vg0604237628 sf0604236629 6 4237628 NA 6.81E-15
vg0604373917 sf0604372918 6 4373917 NA 2.17E-13
vg0604439758 sf0604438759 6 4439758 NA 5.65E-13
vg0604317901 sf0604316902 6 4317901 NA 4.12E-11
vg0701270194 sf0701269194 7 1270194 NA 4.40E-09
vg0601465470 sf0601464471 6 1465470 NA 1.33E-08
vg0604303918 sf0604302919 6 4303918 NA 1.73E-08
vg1114197693 sf1113734014 11 14197693 NA 1.09E-07
vg0601481283 sf0601480284 6 1481283 NA 1.17E-07
vg0803502519 sf0803501522 8 3502519 NA 1.41E-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).


TOC

Navigation