Abstract

High-density genome-wide genotyping using SNPs is becoming the pervasive technology for marker-assisted breeding and population characterization of important crops, due to the advantages in the speed and cost of SNP markers. At the International Rice Research Institute (IRRI), two research programs are generating SNP genotyping data using next-generation sequencing (NGS) technologies, high-throughput SNP platforms such as the Illumina BeadXpress and Fluidigm EP1 systems, and Affymetrix® chips from the Rice SNP consortium, from various activities such as characterizing diversity of the rice genebank, DNA fingerprinting, QTL mapping, discovery of novel alleles underlying these QTLs, and marker-assisted selection for the breeding program. Seemingly trivial tasks such as viewing SNPs positions, subsetting and transposing SNP genotype matrices for genetic mapping and association analyses software have become overwhelming tasks for breeders and molecular biologists, requiring the use of specialized bioinformatics software with command-line interfaces. Equivalent commercial software with easy-to-use graphical user interfaces (GUI) usually cost thousands of dollars. In the human genomics community, the Open Source web application, Galaxy, has provided GUIs and workflow management of standard and often repetitive bioinformatics analysis tasks. We adopted Galaxy as bioinformatics resource, and added in-house developed software specific for rice research such as Alchemy SNP allele calling (Wright et al) for Beadstudio platforms, SNP data reformatting for compatibility with genetic mapping/diversity analyses applications, and management of huge data matrices. The IRRI Galaxy resource is freely accessible, and other Galaxy installations can download the specialized tools in the resource via the IRRI Galaxy TOOLSHED site under development.