Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

By N. Baird, Paul D. Etter, T. S. Atwood, M. Currey, A. Shiver, Zachary A. Lewis, E. Selker, W. Cresko, Eric A. Johnson. PLoS ONE, 2008

3,361 citations recorded by the source corpus.

Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e18b33f5428ff9a4dd7c26e4c569245c5acc1ee1

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Citations in the corpus

Hybridisation between native Oreochromis species and introduced Nile tilapia O. niloticus in the Kafue River, Zambia (2014, background): “…the Kafue fishery region, as well as exhaustive surveys of the entire genome (e.g. by Restriction enzyme Amplified DNA marker sequencing (RAD-tags); Baird et al. 2008) are needed to determine more accurately the degree of hybridisation and introgression occurring, and the cause(s) for departures…”
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species (2011, neutral): “associated DNA (RAD) tags [20].”
Natural variations and genome-wide association studies in crop plants. (2014, methodology): “, using SbfI or EcoRI) and sequence them to identify polymorphic markers (6).”
Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, background): “It was inspired by the whole genome sequence effort in rice [2] and builds upon the protocol of restriction site-associated DNA (RAD) tags [12].”
Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics (2019, methodology): “The protocols vary on a few major axes; first, a protocol may employ one (GBS; Elshire et al., 2011; single‐digest RAD, sdRAD; Baird et al., 2008; BestRAD; Ali et al., 2016) or two restriction enzymes (CRoPS; van Orsouw et al., 2007; double‐digest RAD; Peterson, Weber, Kay, Fisher, & Hoekstra,…”
Species Delimitation: A Decade After the Renaissance (2013, positive): “NGS technol‐ ogies have been recently applied to development of thousands of gene regions spanning multiple divergence times [78], or loci targeted for “shallow-scale” phylogenetic/phylogeo‐ graphic studies [79], and microsatellites [80] or SNPs [81] for extremely shallow phylogeo‐”
Ecological genetics of invasive alien species (2011, methodology): “In particular, the RAD-tag method (Baird et al. 2008) allows an unprecedented number of genetic markers to be characterised and typed, offering a powerful means to identify loci contributing to adaptation during invasions (see Hohenlohe et al. 2010 for a recent application and Stapley et al. 2010…”
Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “…on a narrower subset of these approaches, collectively known as ‘reduced representation’ methods, which include varieties of restriction enzyme-based (Baird et al. 2008; Elshire et al. 2011; Peterson et al. 2012), transcriptomic (Dunn et al. 2008; Smith et al. 2011; Misof et al. 2014) and targeted…”
SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing (2013, background): “Most other sequence-based genotyping methods cannot do this [18,22].”