A high-throughput restriction-site associated DNA sequencing protocol with associated results summarization pipeline

Genome-wide SNP detection is essential for numerous procedures in advanced genome analyses. We have developed an efficient RAD-Seq experimental protocol incorporating simultaneous double restriction digestion and adaptor ligation using novel adaptors to read index and restriction-site free genome sequences separately, which allows the use of standard Illumina library sequencing protocols to enhance efficiency. In addition, we have developed a pipeline for summarization of the derived data in an easy to use HTML format, and have verified the utility of our protocol using a case study of geographically dispersed plants. We expect that our protocol and summary report will likely be a powerful tool to analyze large number of samples derived from various species.