An industry friendly, inexpensive DNA extraction method for Penaeid shrimp that is compatible with Sequenom® iPLEX Platinum SNP pedigree genotyping platforms

This paper reports on an industry-friendly, inexpensive DNA extraction method for Penaeid shrimp that is compatible with Sequenom® iPLEX Platinum SNP pedigree genotyping platforms. The DNA extraction method employed MicroGEM’s commercial prepGEM™ DNA extraction kit in combination with water bath ultrasonic disruption. Two prepGEM™ enzyme concentrations were compared; 100% and 10% of the manufacturer’s recommendation. The utility of the method was compared to a more expensive DNeasy® extraction kit (QIAGEN, Hilden, Germany) by looking at DNA quality and yield from shrimp pleopod tips (approximately 3 mm2 in size) and SNP call rates when DNA was run on a Sequenom® iPLEX Platinum pedigree genotyping panel. DNA from all methods (inexpensive and expensive) was of sufficient quality and quantity for multiplex PCR discrimination of SNP markers in a single Sequenom™ Platinum chemistry panel. This paper demonstrates that the inexpensive MicroGEM (referenced as ‘ZyGEM’) DNA extraction method will provide significant cost-savings to commercial operations that perform routine genotyping within breeding programs, and potentially broadening the use of DNA markers for commercial enterprises.