title: Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences.
abstract: The application of next-generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome-wide and gene-based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high-throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.
authors.affiliation: U. S. Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, Wisconsin 53706, USA. jezalapa@wisc.edu
authors.forename: Juan E
authors.initials: JE
authors.lastname: Zalapa
authors.forename: Hugo
authors.initials: H
authors.lastname: Cuevas
authors.forename: Huayu
authors.initials: H
authors.lastname: Zhu
authors.forename: Shawn
authors.initials: S
authors.lastname: Steffan
authors.forename: Douglas
authors.initials: D
authors.lastname: Senalik
authors.forename: Eric
authors.initials: E
authors.lastname: Zeldin
authors.forename: Brent
authors.initials: B
authors.lastname: McCown
authors.forename: Rebecca
authors.initials: R
authors.lastname: Harbut
authors.forename: Philipp
authors.initials: P
authors.lastname: Simon
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D018742:DNA, Chloroplast / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D056426:Genetic Loci; D060005:Genotyping Techniques; D018895:Microsatellite Repeats; D008928:Mitochondria / Q000235:genetics; D008969:Molecular Sequence Data; D018087:Plastids / Q000235:genetics; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D059467:Transcriptome; D029799:Vaccinium macrocarpon / Q000235:genetics
chemical_list: D018742:DNA, Chloroplast; D004272:DNA, Mitochondrial; D018744:DNA, Plant