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 mr1586 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
vg1005695540 sf1005712078 10 5695540 8.09E-45 2.96E-11
vg1010636917 sf1010565738 10 10636917 1.82E-38 4.31E-10
vg0434705432 sf0434520321 4 34705432 1.70E-36 4.56E-07
vg1226954152 sf1226920551 12 26954152 5.15E-34 NA
vg0327439642 sf0327432695 3 27439642 5.21E-34 5.12E-12
vg0327391604 sf0327384657 3 27391604 7.45E-34 2.70E-10
vg1201753612 sf1201752609 12 1753612 2.37E-33 3.62E-08
vg0911246065 sf0911245064 9 11246065 3.80E-30 7.94E-10
vg0911039399 sf0911038398 9 11039399 1.47E-28 3.78E-08
vg0331362532 sf0331355417 3 31362532 1.90E-27 NA
vg0335000939 sf0334993809 3 35000939 3.93E-25 NA
vg0327424324 sf0327417377 3 27424324 NA 2.55E-19
vg0327425445 sf0327418498 3 27425445 NA 6.57E-18
vg1005967804 sf1005984342 10 5967804 NA 2.99E-15
vg0317023117 sf0317021991 3 17023117 NA 3.78E-15
vg0324795678 sf0324793757 3 24795678 NA 4.61E-15
vg0222830353 sf0222824484 2 22830353 NA 8.22E-13
vg1005694637 sf1005711175 10 5694637 NA 5.44E-12
vg0628001136 sf0628000138 6 28001136 NA 1.16E-11
vg0628049712 sf0628048714 6 28049712 NA 1.13E-10
vg0202735231 sf0202735229 2 2735231 NA 7.63E-10
vg0304861604 sf0304860606 3 4861604 NA 8.00E-10
vg0227637893 sf0227632024 2 27637893 NA 8.77E-10
vg0400468558 sf0400467556 4 468558 NA 8.88E-10
vg0222778846 sf0222772977 2 22778846 NA 1.02E-09
vg0907825976 sf0907824976 9 7825976 NA 1.27E-09
vg0220269450 sf0220263582 2 20269450 NA 2.66E-09
vg0628029397 sf0628028399 6 28029397 NA 3.69E-09
vg1009564247 sf1009493068 10 9564247 NA 5.02E-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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