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 mr1841 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
vg1124468452 sf1124002292 11 24468452 1.42E-22 1.41E-17
vg1125147847 sf1124681687 11 25147847 2.24E-19 8.54E-19
vg0815631643 sf0815628929 8 15631643 5.87E-14 1.46E-10
vg1124331341 sf1123865211 11 24331341 7.84E-14 1.41E-13
vg1124341241 sf1123875085 11 24341241 1.58E-13 1.62E-11
vg1124965681 sf1124499521 11 24965681 4.10E-13 2.20E-13
vg0811525476 sf0811524481 8 11525476 1.87E-12 2.35E-06
vg1124348003 sf1123881847 11 24348003 2.70E-12 1.80E-09
vg0113026938 sf0113025912 1 13026938 2.11E-11 2.71E-07
vg1206990413 sf1206989303 12 6990413 3.48E-11 9.61E-09
vg0812016101 sf0812015106 8 12016101 5.75E-11 1.91E-07
vg1127802372 sf1127330758 11 27802372 8.00E-11 3.46E-12
vg1123203627 sf1122737498 11 23203627 8.49E-11 2.60E-10
vg0503762591 sf0503762568 5 3762591 1.80E-10 5.11E-09
vg1015983381 sf1015912153 10 15983381 2.18E-10 4.59E-08
vg1124340538 sf1123874382 11 24340538 7.24E-10 5.25E-08
vg0521578860 sf0521511524 5 21578860 7.59E-10 1.86E-08
vg1125116625 sf1124650465 11 25116625 2.60E-08 3.79E-08
vg0102329091 sf0102328091 1 2329091 7.69E-08 1.22E-07
vg0520747897 sf0520685338 5 20747897 1.80E-07 6.52E-08
vg0224288814 sf0224282945 2 24288814 3.93E-07 1.98E-07
vg1124950335 sf1124484175 11 24950335 1.27E-06 1.80E-07
vg1125108494 sf1124642334 11 25108494 NA 5.37E-07
vg0213822496 sf0213816626 2 13822496 NA 4.60E-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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