Automated High-Throughput SNP Genotyping from Zea mays

Increases in the efficient use of economically important crops are required to keep pace with increasing world human population and global development.  To help accomplish this, plant genetics, specifically high throughput identification of single nucleotide polymorphisms (SNPs) associated with increased food and energy production phenotypes leading to selection and breeding of beneficial genetic traits are needed.  Here we describe a beginning-to-end automated process for SNP identification in the genome pf Zea mays, otherwise known as maize, or corn. Plant material DNA extraction and DNA quantity normalization were performed with Omega Bio-tek’s Mag-Bind® Plant DNA DS 96 kit and Mag-Bind® EquiPure gDNA Normalization kit. Both of these processes are accomplished using a custom script program on Hamilton’s open liquid handling platform, the Microlab STAR. Finally, the SNP content of the corn genome was rapidly and accurately determined by the combination of Fluidigm’s Juno™ system for sample set up and EP1 system for digital end-point PCR analysis. This entire customized and automated process is able to identify 96 SNPs from corn leaf samples in 5 hours starting with as little as 7 ng of gDNA per sample. In summary, we present an automation friendly workflow for high throughput sample extraction, genomic DNA normalization, and SNP genotyping that can be applied to a variety of sample types and downstream genotyping applications.