Association Discovery & Data Integration
(CoA 4, 5)

Examples of analyses already done in reference panel

• • Pilot studies on reference panel

Benchmarking results

• • Results of GWAS methods benchmarking for MAGIC ref panel (link)

  • Recommended analyses methods for GWAS (link)

  • Multi-environment GWAS methods (link)

    • Manhattan bubble representation of GWAS results across sites (Spindel, PAG 2018)

Tools. (ongoing development)

• • CropGalaxy tools:

    • A GWAS based pipeline (using GEMMA MLM and PLINK)

    • BGLR package

  • GRA - GigWA: with RefPanel SNPs (LOGIN required ; email <p.larmande@ird.fr>)

  • ***B4R for GRA

Main web resources links (NOT GRA-customized)

The following are resources and databases useful for working with rice. These do not (yet) have GRA datasets pre-loaded, but can be used i

• B4R: Trial management and Phenotyping data

• SNP-Seek: Genotypes, panel, GWAS viewer

• GIGWA : Genotypes, panel, analysis

• Galaxy: CropGalaxy instance combines both former Excellence in Breeding Galaxy and IRRI's RIceGalaxy, giving access to tools from both instances

  • Galaxy Excellence in Breeding: Data analysis workflows for QTL , GWAS, etc...

  • Galaxy IRRI : Data analysis workflows for Genomics/HT Genotypes, GxE, etc...