Genotyping with nextRAD markers allows next-generation sequencing reads to pile up at loci scattered across the genome, giving high-quality SNP calls. It differs from other genotyping-by-sequencing methods by not using restriction enzymes to sample only a portion of the genome. Instead, it uses selective primers to amplify only the loci in the genome with the selective sequence. The small number of steps in the protocol reduces loss during library creation, allowing much lower input compared to other methods.


Here is a sampling of early nextRAD publications, showing utility for low-input samples and a wide variety of species:
From promise to practice: pairing non-invasive sampling with genomics in conservation
Deep reefs are not universal refuges: Reseeding potential varies among coral species
Using NextRAD sequencing to infer movement of herbivores among host plants
Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna

nextRAD method


Selective primers productively amplify only fragments with the selective sequence at the end. Subsequent sequencing of the library allows determination of genetic variation at these loci.