The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century1

Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.

[1]  Charlotte C. Germain-Aubrey,et al.  A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes1 , 2016, Applications in Plant Sciences.

[2]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[3]  L. Knowles,et al.  Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences. , 2016, Systematic biology.

[4]  G. Luikart,et al.  Harnessing the power of RADseq for ecological and evolutionary genomics , 2016, Nature Reviews Genetics.

[5]  Matthew A. Gitzendanner,et al.  The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae , 2016, Front. Plant Sci..

[6]  M. Nowak,et al.  Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae) , 2015, PloS one.

[7]  James B. Beck,et al.  Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)1 , 2015, Applications in plant sciences.

[8]  Pascal Hingamp,et al.  QDD version 3.1: a user‐friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate , 2014, Molecular ecology resources.

[9]  Xiao Sun,et al.  Data access for the 1,000 Plants (1KP) project , 2014, GigaScience.

[10]  J. DaCosta,et al.  Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol , 2014, PloS one.

[11]  Na Wei,et al.  The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio , 2014, Molecular ecology resources.

[12]  M. Gardner,et al.  Microsatellite markers from the Ion Torrent: a multi‐species contrast to 454 shotgun sequencing , 2014, Molecular ecology resources.

[13]  Development and evaluation of microsatellite markers for the gynodioecious shrub Daphne jezoensis (Thymelaeaceae)1 , 2014, Applications in plant sciences.

[14]  Shizhong Xu,et al.  Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd. , 2014, The Plant journal : for cell and molecular biology.

[15]  N. Mills,et al.  iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries , 2014, BMC Genomics.

[16]  M. Bayer,et al.  An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley , 2014, BMC Genomics.

[17]  Marcus Frohme,et al.  Microsatellite marker discovery using single molecule real-time circular consensus sequencing on the Pacific Biosciences RS. , 2013, BioTechniques.

[18]  Mark P. Miller,et al.  SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data. , 2013, The Journal of heredity.

[19]  Mohd Y. Rafii,et al.  A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance , 2013, International journal of molecular sciences.

[20]  Fengtang Yang,et al.  Fine Mapping of the Pond Snail Left-Right Asymmetry (Chirality) Locus Using RAD-Seq and Fibre-FISH , 2013, PloS one.

[21]  Susan McCouch,et al.  Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations , 2013, Theoretical and Applied Genetics.

[22]  Peng Lu,et al.  GMATo: A novel tool for the identification and analysis of microsatellites in large genomes , 2013, Bioinformation.

[23]  T. Cezard,et al.  The effect of RAD allele dropout on the estimation of genetic variation within and between populations , 2013, Molecular ecology.

[24]  Russell B. Corbett-Detig,et al.  RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling , 2013, Molecular ecology.

[25]  S. Narum,et al.  Genotyping‐by‐sequencing in ecological and conservation genomics , 2013, Molecular ecology.

[26]  C. Robin Buell,et al.  Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing , 2013, Genetics.

[27]  V. Chand,et al.  Isolation and characterization of 21 polymorphic microsatellite loci in the iconic Australian lungfish, Neoceratodus forsteri, using the Ion Torrent next-generation sequencing platform , 2013, Conservation Genetics Resources.

[28]  H. Hartikainen,et al.  Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing , 2013, Journal of evolutionary biology.

[29]  Benjamin J. Wainwright,et al.  Isolation and characterization of twenty-one polymorphic microsatellite loci for Polycarpa aurata using third generation sequencing , 2013, Conservation Genetics Resources.

[30]  Noah A. Rosenberg,et al.  The Relationship Between FST and the Frequency of the Most Frequent Allele , 2013, Genetics.

[31]  Brian Boyle,et al.  An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping , 2013, PloS one.

[32]  Robert J. Elshire,et al.  Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol , 2013, PLoS genetics.

[33]  T. Cezard,et al.  Special features of RAD Sequencing data: implications for genotyping , 2012, Molecular ecology.

[34]  H. Dalgleish,et al.  A conceptual framework for restoration of threatened plants: the effective model of American chestnut (Castanea dentata) reintroduction. , 2013, The New phytologist.

[35]  N. Bassil,et al.  Microsatellite Marker Development in Peony using Next Generation Sequencing , 2013 .

[36]  José Crossa,et al.  Genomic Selection in Wheat Breeding using Genotyping‐by‐Sequencing , 2012 .

[37]  Trevor W. Rife,et al.  Genotyping‐by‐Sequencing for Plant Breeding and Genetics , 2012 .

[38]  Haofeng Chen,et al.  HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data , 2012, Bioinform..

[39]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[40]  Todd A. Castoe,et al.  Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake , 2012, PloS one.

[41]  Douglas Senalik,et al.  Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. , 2012, American journal of botany.

[42]  P. J. Maughan,et al.  Targeted enrichment strategies for next-generation plant biology. , 2012, American journal of botany.

[43]  S. Haig,et al.  Multiplexed microsatellite recovery using massively parallel sequencing , 2011, Molecular ecology resources.

[44]  M. Gardner,et al.  Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development , 2011, Molecular ecology resources.

[45]  T. Glenn.  Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.

[46]  A. Guggisberg,et al.  RAD in the realm of next‐generation sequencing technologies , 2011, Molecular ecology.

[47]  O. Lepais,et al.  De novo discovery and multiplexed amplification of microsatellite markers for black alder (Alnus glutinosa) and related species using SSR-enriched shotgun pyrosequencing. , 2011, The Journal of heredity.

[48]  R. Petit,et al.  Current trends in microsatellite genotyping , 2011, Molecular ecology resources.

[49]  M. Blaxter,et al.  Genome-wide genetic marker discovery and genotyping using next-generation sequencing , 2011, Nature Reviews Genetics.

[50]  Robert J. Elshire,et al.  A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species , 2011, PloS one.

[51]  Tina T. Hu,et al.  Multiplexed shotgun genotyping for rapid and efficient genetic mapping. , 2011, Genome research.

[52]  P. Etter,et al.  SNP discovery and genotyping for evolutionary genetics using RAD sequencing. , 2011, Methods in molecular biology.

[53]  M. Rai,et al.  Microsatellite markers: an overview of the recent progress in plants , 2011, Euphytica.

[54]  Chun Liang,et al.  An annotated genetic map of loblolly pine based on microsatellite and cDNA markers , 2011, BMC Genetics.

[55]  M. Blaxter,et al.  RADSeq: next-generation population genetics. , 2010, Briefings in functional genomics.

[56]  D. Grattapaglia,et al.  Positioning of the major locus for Puccinia psidii rust resistance (Ppr1) on the Eucalyptus reference map and its validation across unrelated pedigrees , 2010, Tree Genetics & Genomes.

[57]  Robert P. St.Onge,et al.  Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples , 2010, Nucleic acids research.

[58]  Wanjun Gu,et al.  Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence , 2010, Molecular ecology resources.

[59]  Nicholas Stiffler,et al.  Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags , 2010, PLoS genetics.

[60]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[61]  Lars Kraemer,et al.  STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design , 2009, BMC Bioinformatics.

[62]  D. A. Palmieri,et al.  SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation , 2008, International journal of plant genomics.

[63]  B. Faircloth,et al.  msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design , 2008, Molecular ecology resources.

[64]  H. Fukuoka,et al.  A protocol for the construction of microsatellite enriched genomic library , 2006, Plant Molecular Biology Reporter.

[65]  Ych-chu Wang.  Molecular ecology , 1992, Journal of Northeast Forestry University.

[66]  L. Keller,et al.  Back to the future: museum specimens in population genetics. , 2007, Trends in ecology & evolution.

[67]  Robert J Toonen,et al.  Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. , 2006, Ecology letters.

[68]  W. Amos,et al.  Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion , 2004, Molecular ecology.

[69]  H. Ellegren.  Microsatellites: simple sequences with complex evolution , 2004, Nature Reviews Genetics.

[70]  J. A. Buso,et al.  Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.) , 2004, BMC Plant Biology.

[71]  H. Nybom,et al.  Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method , 2004, Theoretical and Applied Genetics.

[72]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[73]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[74]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[75]  E. Nevo,et al.  Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review , 2002, Molecular ecology.

[76]  A. Rafalski.  Applications of single nucleotide polymorphisms in crop genetics. , 2002, Current opinion in plant biology.

[77]  Guang R. Gao,et al.  TROLL-Tandem Repeat Occurrence Locator , 2002, Bioinform..

[78]  L. Zane,et al.  Strategies for microsatellite isolation: a review , 2002, Molecular ecology.

[79]  H. Ellegren.  Microsatellite mutations in the germline: implications for evolutionary inference. , 2000, Trends in genetics : TIG.

[80]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[81]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[82]  A. Estoup,et al.  Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species , 1998, Journal of Molecular Evolution.

[83]  D. Soltis,et al.  Molecular Systematics of Plants II , 1998, Springer US.

[84]  M Slatkin,et al.  A measure of population subdivision based on microsatellite allele frequencies. , 1995, Genetics.

[85]  G. Lathrop,et al.  Rat gene mapping using PCR-analyzed microsatellites. , 1992, Genetics.

[86]  Kitae Song,et al.  Applications in Plant Sciences , 2022 .