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 mr1601 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
vg0805464731 sf0805463734 8 5464731 1.57E-44 2.58E-07
vg0820068882 sf0820066169 8 20068882 4.40E-44 1.71E-06
vg0626823814 sf0626822817 6 26823814 6.95E-44 NA
vg0624629287 sf0624628290 6 24629287 5.78E-43 4.95E-06
vg0916955985 sf0916954984 9 16955985 6.20E-43 NA
vg1218887444 sf1218858879 12 18887444 1.41E-42 8.51E-07
vg0826953770 sf0826951056 8 26953770 3.64E-42 5.42E-07
vg0720010188 sf0720009195 7 20010188 1.22E-41 1.39E-07
vg1214354909 sf1214352249 12 14354909 NA 1.49E-07
vg0719091461 sf0719090468 7 19091461 NA 5.42E-07
vg1124032771 sf1123566641 11 24032771 NA 7.73E-07
vg0114635543 sf0114634517 1 14635543 NA 1.54E-06
vg1217896822 sf1217868256 12 17896822 NA 1.80E-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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