Microsatellites, or simple sequence repeats (SSRs), are short repeated DNA motifs (typically one to six nucleotides) located throughout eukaryotic genomes ( Li et al., 2002 Zane et al., 2002). We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. 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). 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. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism.
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