RAD-Seq

Restriction-Site Associated DNA Sequencing

RAD-seq is a protocol for genotyping and discovery of single-nucleotide polymorphisms (SNPs) (Baird et al., 2008). This approach is particularly useful for genotyping when a reference genome is not available, such as in ecological studies (Andrews et al., 2016). PE RAD-seq, also called RAD-PE, is the same protocol as RAD but uses paired-end sequencing for improved alignments (Willing et al., 2011). Several variations, such as ddRADseq (Peterson et al., 2012), 2b-RAD (Wang et al., 2012), SLAF-seq (Sun et al., 2013), and hyRAD (Suchan et al., 2016) have been developed to address specific applications, and multiple software packages are available to analyze RAD data (Fan et al., 2016) (Catchen et al., 2013).

In this method, genomic DNA (gDNA) is first digested with a restriction enzyme and a barcoded P1 adapter is ligated to the fragments. The adapter-ligated fragments from different samples are combined, if samples are multiplexed, and the DNA is sheared. The fragments are size-selected and purified. The P2 adapter-primers are ligated and the fragments are amplified to produce the sequencing library.

Advantages:

  • No reference genome required (Reitzel et al., 2013)
  • Relatively inexpensive, compared to whole-genome sequencing
  • The degree of genome coverage can be adjusted by selecting various restriction enzymes and fragment sizes

Disadvantages:

  • There can be gaps in the genome coverage
  • Requires high-quality DNA (see hyRAD for low-quality DNA) (Suchan et al., 2016)
  • Sequence polymorphism at the DNA restriction sites causes a progressive loss of shared restriction sites among diverging clades (Suchan et al., 2016)


Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81-92

da Fonseca R. R., Albrechtsen A., Themudo G. E., et al. Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Mar Genomics. 2016;30:3-13

Kagale S., Koh C., Clarke W. E., Bollina V., Parkin I. A. and Sharpe A. G. Analysis of Genotyping-by-Sequencing (GBS) Data. Methods Mol Biol. 2016;1374:269-284

Kim C., Guo H., Kong W., Chandnani R., Shuang L. S. and Paterson A. H. Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Sci. 2016;242:14-22

Manel S., Perrier C., Pratlong M., et al. Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Mol Ecol. 2016;25:170-184

Sanders I. R. and Rodriguez A. Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems. ISME J. 2016;10:2780-2786



References:

Ren P., Peng W., You W., et al. Genetic mapping and quantitative trait loci analysis of growth-related traits in the small abalone Haliotis diversicolor using restriction-site-associated DNA sequencing. Aquaculture. 2016;454:163-170

Wang J., Xue D. X., Zhang B. D., Li Y. L., Liu B. J. and Liu J. X. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus). PLoS One. 2016;11:e0157809

He T., D’Agui H., Lim S. L., Enright N. J. and Luo Y. Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot. Sci Rep. 2016;6:26315

Paun O., Turner B., Trucchi E., Munzinger J., Chase M. W. and Samuel R. Processes Driving the Adaptive Radiation of a Tropical Tree (Diospyros, Ebenaceae) in New Caledonia, a Biodiversity Hotspot. Syst Biol. 2016;65:212-227

Bian C., Hu Y., Ravi V., et al. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci Rep. 2016;6:24501

Clark L. V. and Sacks E. J. TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code Biol Med. 2016;11:11, href=”http://www.ncbi.nlm.nih.gov/pubmed/26691641″ target=”_blank”>Hou Y., Nowak M. D., Mirre V., Bjora C. S., Brochmann C. and Popp M. RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae). Mol Phylogenet Evol. 2015;95:152-160

Diaz-Arce N., Arrizabalaga H., Murua H., Irigoien X. and Rodriguez-Ezpeleta N. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Mol Phylogenet Evol. 2016;102:202-207

Diaz-Arce N., Arrizabalaga H., Murua H., Irigoien X. and Rodriguez-Ezpeleta N. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Mol Phylogenet Evol. 2016;102:202-207

Fan W., Zong J., Luo Z., et al. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding. PLoS One. 2016;11:e0147187

Fernandez R., Schubert M., Vargas-Velazquez A. M., et al. A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins. Mol Ecol Resour. 2016;16:266-276

Herrera S. and Shank T. M. RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Mol Phylogenet Evol. 2016;100:70-79

Jiang N., Zhang F., Wu J., et al. A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. Theor Appl Genet. 2016;129:1739-1757

Manthey J. D. and Robbins M. B. Genomic insights into hybridization in a localized region of sympatry between pewee sister species (Contopus sordidulus _ C. virens) and their chromosomal patterns of differentiation. Avian Research. 2016;7:

Qiu S., Bergero R., Guirao-Rico S., et al. RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region. Mol Ecol. 2016;25:414-430

Ravinet M., Westram A., Johannesson K., Butlin R., Andre C. and Panova M. Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale. Mol Ecol. 2016;25:287-305

Takahashi T. and Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol. 2016;100:234-242

Yang H., Wei C. L., Liu H. W., et al. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PLoS One. 2016;11:e0151424

Yang J., Guo B., Shikano T., Liu X. and Merila J. Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep. 2016;6:26632

Zhao Y., Zhang C., Chen H., et al. QTL mapping for bacterial wilt resistance in peanut (Arachis hypogaea L.). Mol Breed. 2016;36:13

Combosch D. J. and Vollmer S. V. Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol Phylogenet Evol. 2015;

DaCosta J. M. and Sorenson M. D. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol. 2015;

Demos T. C., Kerbis Peterhans J. C., Joseph T. A., Robinson J. D., Agwanda B. and Hickerson M. J. Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles. PLoS One. 2015;10:e0131800

Guo B., DeFaveri J., Sotelo G., Nair A. and Merila J. Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol. 2015;13:19

Liu S., Clark L. V., Swaminathan K., Gifford J. M., Juvik J. A. and Sacks E. J. High-density genetic map ofMiscanthus sinensisreveals inheritance of zebra stripe. GCB Bioenergy. 2016;8:616-630

Longo G. and Bernardi G. The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data. Mol Phylogenet Evol. 2015;88:55-63

Marubodee R., Ogiso-Tanaka E., Isemura T., et al. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich. PLoS One. 2015;10:e0138942

Mathers T. C., Hammond R. L., Jenner R. A., Hanfling B., Atkins J. and Gomez A. Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis. Heredity (Edinb). 2015;

Shao C., Niu Y., Rastas P., et al. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res. 2015;

Takahashi T. and Moreno E. A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol Phylogenet Evol. 2015;

Tennessen J. A., Bonner K. M., Bollmann S. R., et al. Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni. PLoS Negl Trop Dis. 2015;9:e0004077

Yu S., Chu W., Zhang L., et al. Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing. PLoS One. 2015;10:e0131572

Zhou Z., Liu S., Dong Y., et al. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing. PLoS One. 2015;10:e0138585