The Report of My Death was an Exaggeration: A Review for Researchers Using Microsatellites in the 21st Century

• Published in: Applications in plant sciences Vol. 4; no. 6
• Main Authors: Hodel, Richard G. J, Segovia-Salcedo, M. Claudia, Landis, Jacob B, Crowl, Andrew A, Sun, Miao, Liu, Xiaoxian, Gitzendanner, Matthew A, Douglas, Norman A, Germain-Aubrey, Charlotte C, Chen, Shichao, Soltis, Douglas E, Soltis, Pamela S
• Format: Journal Article
• Language: English
• Published: United States Botanical Society of America 01.06.2016; John Wiley & Sons, Inc
• Subjects: chromosome mapping; Computer programs; computer software; Conservation genetics; cost effectiveness; Costs; Deoxyribonucleic acid; DNA; DNA sequencing; Estimates; Forensic science; forensic sciences; Gene mapping; Gene polymorphism; Genetic markers; Genomes; Genotyping; genotyping by sequencing (GBS); high-throughput nucleotide sequencing; microsatellite development; microsatellite repeats; Microsatellites; Mutation; next-generation sequencing (NGS); parentage; phylogeography; Plant sciences; Polymorphism; Polyploidy; Population genetics; Primers; Researchers; restriction site associated DNA sequencing (RAD-Seq); Review; REVIEW ARTICLE; Reviews; Simple sequence repeats; simple sequence repeats (SSR); Studies; transcriptomes; Oregon; United States > US; transcriptomes; genotyping by sequencing (GBS); microsatellite development; restriction site associated DNA sequencing (RAD-Seq); next-generation sequencing (NGS); simple sequence repeats (SSR)
• ISSN: 2168-0450; 2168-0450
• DOI: 10.3732/apps.1600025

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.