We proposed to store large-scale genotype data as integer sparse matrices, which consumed much fewer computing resources for storage and analysis than traditional approaches. In addition, the raw genotype data could be readily recovered from integer sparse matrices. Utilizing this approach, we stored the genotype data of 1612 Asian cultivated rice accessions and 446 Asian wild rice accessions across 8,584,244 SNP sites in the ECOGEMS database with 310xe2x80x89MB of disk usage. Graphical interface for visualization, analysis and download of SNP data were implemented in ECOGEMS, which made it a valuable resource for rice functional genomic studies.