Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.

By Michael R. Miller, J. Dunham, A. Amores, W. Cresko, Eric A. Johnson. Genome Research, 2007

979 citations recorded by the source corpus.

Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/158844853a5a33f93393dd9c2a879c9a234adde5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. A. Singh
2. B. Singh
3. Richard H. Ree
4. J. Davey
5. Mark L. Blaxter
6. C. Moreau
7. B. E. Rubin
8. Jun Wen

In Plant Science

1. Pierre Legendre
2. Jun Wen
3. A. Singh
4. B. Singh
5. Kazusa Kamatari
6. G. Yue
7. Sachiko Isobe
8. David B. Neale

Citations in the corpus

• Continental‐scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides) (2013, methodology): “We also recommend that high-throughput sequencing approaches (e.g. restriction site associated DNA markers; Miller et al., 2007) and common-garden studies (e.”
• Inferring Phylogenies from RAD Sequence Data (2012, methodology): “RAD was initially developed for large-scale microarray-based genotyping in two model organisms, the threespine stickleback (Gasterosteus aculeatus) and the fungus Neurospora crassa [9–11].”
• Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags (2010, methodology): “We used a novel and efficient genotyping approach based on Illumina sequencing of libraries of Restriction-site Associated DNA (RAD) tags [98,99].”
• Stickleback research: the now and the next (2013, methodology): “Numerous genomic tools have been developed specifically for stickleback and multiple stickleback genomes have been sequenced (Peichel et al., 2001; Kingsley et al., 2004; Kingsley and Peichel, 2007; Miller et al., 2007b; Baird et al., 2008; Hohenlohe et al., 2010, 2012b; Jones et al., 2012a, 2012b).”
• Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, methodology): “This method has proven effective at generating data for marker development (Miller et al., 2007), genome scans (Hohenlohe et al., 2010), and building distance-based phylogenies for recent demographic events (Emerson et al., 2010).”
• Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach (2012, neutral): “The use of genome complexity reduction combined with multiplex sequencing was first demonstrated through restrictionsite associated DNA (RAD) tagging [16,17] and NGS of the RAD tags to genetically map mutations [18].”
• Special features of RAD Sequencing data: implications for genotyping (2012, methodology): “Restriction site-associated DNA sequencing (RAD-Seq; Miller et al. 2007; Baird et al. 2008; Davey & Blaxter 2011) is a method for SNP discovery and genotyping using sequencing-by-synthesis.”
• Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations (2017, background): “…approaches to obtain genome-wide markers such as Single Nucleotide Polymorphisms (SNPs) include Restriction-site Associated DNA Sequencing (RADseq, Miller et al. 2007) or Genotype by Sequencing (GBS, Elshire et al. 2011; Narum et al. 2013) and target enrichment (Dasgupta et al. 2015; Lu et al.…”
• Recent advances of genome mapping and marker‐assisted selection in aquaculture (2013, background): “RAD tags are the genomic DNA sequences immediately flanking each instance of a particular restriction enzyme cutting site on the whole genome (Miller et al. 2007).”
• REVIEW: PART OF A HIGHLIGHT ON BREEDING STRATEGIES FOR FORAGE AND GRASS IMPROVEMENT Will genomic selection be a practical method for plant breeding? (2012, background): “The former includes SNP, DArT, GBS and RAD markers while the latter include SSR, RAPD (random amplified polymorphic DNA) and RFLP (restriction fragment length polymorphism) markers.”
• Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate (2013, methodology): “Such associations using high-resolution genome-wide scans are now feasible for non-model species, due to the emergence of reduced-representation DNA library sequencing using restriction-enzymes (e.g., Davey et al. 2011; Elshire et al. 2011; Miller et al. 2007).”