Selective breeding in shrimp aquaculture has transformed a multi-billion dollar industry. The challenge it creates is routine, affordable genotyping, identifying which individuals carry the genetic markers that breeders are selecting for, at the scale of hundreds of thousands of animals per cycle.

A study published in Aquaculture compared prepGEM Insect chemistry with the QIAGEN DNeasy kit for DNA extraction from Penaeid shrimp pleopod tips: approximately 3 mm² of tissue per animal. DNA from both methods was run on a Sequenom iPLEX Platinum SNP genotyping panel.

Both methods produced DNA of sufficient quality and quantity for multiplex SNP discrimination. The prepGEM method combined with ultrasonic disruption provided the same call rates as the more expensive DNeasy protocol, at significantly lower cost per sample.

The authors concluded that the method would provide meaningful cost savings to commercial operations performing routine genotyping within breeding programmes, and could broaden the adoption of DNA-based selection in aquaculture enterprises that currently find per-sample costs prohibitive.