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Advancement of  genomics boosts the production of sequence data resulting in so-called bio bigdata. Currently, in NCBI,  46 Tera-bases have been deposited facilitating genome-driven breeding programs. The sample space of major crops like soybean consisted largely with modern cultivars resulted from well-designed breeding pedigree and it would be critical to understand breeding history of cultivars for dissecting the sequencing results.  However, the pedigree information of cultivars have been recorded by non-systematical ways that makes it difficult to utilize the information into large-scale genome analysis such as genomic selection. Here we integrated the soybean pedigree information into fixed data format and developed web-based database with representative visualization named as Soybean Pedigree Database (SPD) at http://pgl.gnu.ac.kr/. Our database provides intuitive visualization of pedigree tree as well as well-curated cultivar names and pedigrees of international soybean lines in JSON data format that can be directly utilized for integrated genome analysis.