Open AccessThe report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century
Author(s) -
Hodel Richard G. J.,
SegoviaSalcedo M. Claudia,
Landis Jacob B.,
Crowl Andrew A.,
Sun Miao,
Liu Xiaoxian,
Gitzendanner Matthew A.,
Douglas Norman A.,
GermainAubrey Charlotte C.,
Chen Shichao,
Soltis Douglas E.,
Soltis Pamela S.
Publication year - 2016
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.3732/apps.1600025
Subject(s) - microsatellite , biology , genotyping , evolutionary biology , genetics , genome , dna sequencing , computational biology , population genetics , population , allele , genotype , gene , demography , sociology
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.