Automated Size Selection Key for RADseq: PLoS One Publication

Congratulations to Sage Science customer Hopi Hoekstra and her team at Harvard University for their recent publication in PLoS One! Dr. Hoekstra, who works in the Organismic & Evolutionary Biology and the Molecular & Cellular Biology departments at Harvard, reports a full laboratory protocol for RADseq, or reduced-representation genome sequencing for use in population genotyping. The method allows for studying hundreds of thousands of markers across hundreds of individuals or more.

The paper, published on May 31 and entitled “Double Digest RADseq: An Inexpensive Method for De NovoSNP Discovery and Genotyping in Model and Non-Model Species,” can be found here. (link to paper)

The authors write: “Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours.”

As part of the library prep protocol, the Harvard team tested out manual gel extraction versus the Pippin Prep for size selection. The paper reports that manual gel excision did not perform as well as automated size selection, “likely because [gel excision] was imprecise or ‘leaky.’” The authors note that for manual gel electrophoresis, “careful practitioners can achieve roughly 50% of the precision and repeatability of automated DNA size selection.”

For more on the Hoekstra lab, click here. (link to her lab)

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