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 to store these data types at the needed scale. Additionally, products are often not designed for the requirements of aquaculture (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 formatted and 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 store and retrieve genotype, phenotype, and pedigree data. Genotypes for biallelic markers are efficiently stored by internally converting them to bitwise representations. Genotypes for multiallelic markers are internally represented as integers and automatically interface with a table of text representations for simple import/export. Genotype data can be stored for haploid, diploid, or polyploid individuals. Pedigree, phenotype, and genotype data are all stored in the same database, which simplifies the process of exporting data for analysis.