MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines

With the rapid decreasing of sequencing cost, large volume of genotype data has been generated in many organisms based on high-throughput sequencing, which was utilized in various fields of biological studies in the post-genome era. The raw sequencing data were usually deposited in the NCBI SRA database. Construction of the database to store and analyze the processed genotype data is an essential step for the utilization of the genotype data by the community. Up to now, a comprehensive genotype database is still missing from maize, which is an important crop of the world. We report the construction of the MaizeSNPDB database using genotype data of 1210 maize line across 35,370,939 SNP sites refined from a large set of genomic variations reported by the maize HapMap 3 project. We further implemented several genetic analysis programs as graphical interfaces in the MaizeSNPDB database. SNPs in user-specified genomic regions could be easily extracted and analyzed in MaizeSNPDB. The whole dataset and code of MaizeSNPDB is available at https://github.com/venyao/MaizeSNPDB. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The MaizeSNPDB database is of great value to future maize functional genomic studies, which can also facilitate marker-assisted breeding in maize.