Abstract
High throughput genotyping technologies are required for large-scale population genetics. Evolutionary biology studies, human disease research and large-scale agricultural breeding programs all lend themselves to technologies that are able to provide more information at lower cost. Over the past decade, genotyping technology has transitioned from PCR-based SNP assays to microarrays, and is now shifting toward high-throughput genotyping by sequencing (GBS). The RipTide High Throughput Rapid DNA Library Prep allows for the preparation of NGS libraries from up to 960 individually barcoded samples in a few hours with automation. When combined with low coverage sequencing and imputation-based genotype analysis, the result is an order of magnitude greater information at a significantly reduced cost. Here we present data on 96 Zea mays (maize) samples consisting of 4 parent populations and 92 recombinant inbred lines (RILs). For each sample, hundreds of thousands to millions of haplotype markers, including SNVs and structural variants, are accurately detected. A minimum of 95% complete coverage of direct and imputed markers is obtained for each RIL. The approach can be applied to any species, regardless of genome size or GC content. In this study, a median of >1 million markers were genotyped by sequencing on an Illumina HiSeq 4000 instrument for an estimated cost of library construction and sequencing of < $25 per sample.