Ultra High-Throughput Genotyping with Crude Plant Samples to Enable Precision Breeding

SNP genotyping is a powerful tool to accelerate breeding programmes for agricultural crop improvements. The crude DNA extracts often used in such high-throughput genotyping projects are rapid and cost-effective to prepare, but can pose significant challenges to downstream analysis due to carry-over of endogenous PCR inhibitors from the original plant material.

The PCR master mix is a key component in determining assay robustness and data quality in PCR-based genotyping. Here we assess the performance of various commercially available PCR master mixes in low-volume, high-throughput SNP genotyping when used with hydrolysis probes. Crude DNA samples from seed or leaf were prepared by a common sodium hydroxide-based extraction protocol. Assays were run on two high-throughput automated genotyping platforms, LGC SNPline^TM using either 384- or 1536-well microtitre plates and Douglas Scientific Nexar^® using 384-well Array Tape^®.