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 mr1757 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
vg0705453437 sf0705452438 7 5453437 1.01E-62 5.14E-23
vg0717004102 sf0717003109 7 17004102 8.32E-43 8.99E-10
vg0622627045 sf0622626048 6 22627045 7.89E-41 1.58E-07
vg0402051720 sf0402047316 4 2051720 3.06E-40 NA
vg0141203398 sf0141202355 1 41203398 6.50E-40 1.78E-07
vg1202743447 sf1202742449 12 2743447 6.64E-36 1.62E-07
vg0808255183 sf0808254187 8 8255183 4.22E-30 1.43E-07
vg0705427326 sf0705426327 7 5427326 NA 1.94E-16
vg0401291884 sf0401287434 4 1291884 NA 1.63E-08
vg0402466598 sf0402462196 4 2466598 NA 3.09E-08
vg0907218440 sf0907217440 9 7218440 NA 3.62E-08
vg1018654414 sf1018582972 10 18654414 NA 6.27E-08
vg0808213475 sf0808212479 8 8213475 NA 6.68E-08
vg0124654977 sf0124653933 1 24654977 NA 7.44E-08
vg0406181895 sf0406177335 4 6181895 NA 1.44E-07
vg0412977243 sf0412967953 4 12977243 NA 1.77E-07
vg0124729720 sf0124728676 1 24729720 NA 1.80E-07
vg0316049074 sf0316047721 3 16049074 NA 2.09E-07
vg1206397770 sf1206396660 12 6397770 NA 2.24E-07
vg0725407361 sf0725406367 7 25407361 NA 2.89E-07
vg0404504944 sf0404500548 4 4504944 NA 3.54E-07
vg0601368496 sf0601367497 6 1368496 NA 3.80E-07
vg0909229224 sf0909228223 9 9229224 NA 3.85E-07
vg0917116253 sf0917115252 9 17116253 NA 3.97E-07
vg0917087568 sf0917086567 9 17087568 NA 5.01E-07
vg0808239790 sf0808238794 8 8239790 NA 1.91E-06
vg0433353615 sf0433168504 4 33353615 NA 2.65E-06
vg0232755756 sf0232749887 2 32755756 NA 6.25E-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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