BnIR Brassica napus multi-omics information resource ————A multi-omics database with various tools for Brassica napus research and breeding

About multi-omics

GWAS, eQTL, and TWAS analyses were performed to identify candidate genes and genetic variants associated with phenotypes based on population-level multiomics data. Using GWAS analysis, we identified a total of 379 genetic loci associated with 55 phenotypes, including 2119 candidate genes. The eQTL analysis of gene expression profiles at 20 and 40 days after flowering identified a total of 4,179,771 genetic variants significantly associated with expression levels of 40,905 genes. A total of 5083 genes significantly associated with 127 phenotypes were identified by TWAS[1]. To more precisely identify the candidate genes significantly associated with phenotypes, we performed co-location analysis and SMR analysis based on GWAS and eQTL analysis results[2,3]. A total of 217 pairs of eQTL and GWAS were identified by co-location analysis. A total of 303 genes with significant phenotypic correlation were identified by SMR analysis[3].

Tutorials for each sub-module

  • GWAS
  • eQTL
  • TWAS
  • SMR
  • Colocalization analysis
  • References

    1. Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BWJH, et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet. 2016; 48:245-252.
    2. Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 2014; 10:e1004383.
    3. Zhu Z, Zhang F, Hu H, Bakshi A, Robinson MR, Powell JE, et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat Genet. 2016; 48:481-487.