An Open Platform Approach for Management and Analysis of Next-Generation Genotyping Data By Breeders and Geneticists

The advent of various affordable nucleotide sequencing technologies caused the shift to use these technologies to generate molecular markers for plant breeding and genetic studies. With thousands to millions of SNP marker data being generated by each assay run, the data deluge has been overwhelming for plant breeders and geneticists, and bioinformaticians need to be engaged to deal with the data and its subsequent analyses. At IRRI, we have adopted user-friendly bioinformatics analyses tools that are publicly available and in prevalent use by the medical and human genetic community to address the data and analyses issues that beset non-bioinformatics-savvy scientists. We chose GALAXY as web application framework for the deployment of these tools, with a customized version currently hosting tools for SNP calling from various genotyping technologies (e.g. Illumina Beadstudio and Infinium, Fluidigm, Affymetrix 700k rice SNP chip, Genotype-by-sequencing, NGS-resequencing) and downstream data manipulation and analysis tools that breeders are already familiar with. Additional tools are being integrated such as TASSEL and R-based GWAS packages. Infrastructure development for systematic data storage will be addressed by systems currently being developed by the International Rice Informatics Consortium (IRIC). These tools will enable breeders and geneticists to directly analyze their data and quickly make decisions from the results.