Breeding programs typically collect genotype, phenotype, and pedigree data in order to inform breeding and programmatic decisions. As programs progress, the cumulative amount of data collected can become substantial. Storing and organizing this data in a manner that facilitates analysis is often challenging because there are few available options that store these data types at the needed scale. Additionally, products are often not designed for the specific needs of aquaculture species (e.g., polyploid genotypes). Programs with sufficient resources may invest in the design of a custom database and rely on a database administrator to oversee its operation. While this is a feasible solution, it has not been universally adopted due to the cost. Many breeders resort to storing data in a series of flat files (e.g., excel spreadsheets, PLINK files, delimited text files) and attempt to maintain consistency across years in how the files are organized. There are obvious drawbacks to this approach as it does not facilitate quality control, standardization, or data access.
To address this problem, an open-source interface was written for the widely available MySQL database management system. The interface works with a standard, freely available version of MySQL to efficiently store and retrieve genotype, phenotype, and pedigree data. Genotypes for biallelic markers are stored by converting them to bitwise representations. Genotypes for multiallelic markers are stored by either representing genotypes or alleles as integers and automatically interfacing with a table matching integers to text representations. Genotype data can be stored for haploid, diploid, or polyploid individuals. Pedigree and phenotype data are stored in the same database as genotype data, which simplifies the process of exporting data for analysis.