title: Current trends in microsatellite genotyping.
abstract: Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.
authors.affiliation: INRA, UMR 1202 Biodiversity Genes & Communities, F-33610 Cestas, France.
authors.forename: E
authors.initials: E
authors.lastname: Guichoux
authors.forename: L
authors.initials: L
authors.lastname: Lagache
authors.forename: S
authors.initials: S
authors.lastname: Wagner
authors.forename: P
authors.initials: P
authors.lastname: Chaumeil
authors.forename: P
authors.initials: P
authors.lastname: Léger
authors.forename: O
authors.initials: O
authors.lastname: Lepais
authors.forename: C
authors.initials: C
authors.lastname: Lepoittevin
authors.forename: T
authors.initials: T
authors.lastname: Malausa
authors.forename: E
authors.initials: E
authors.lastname: Revardel
authors.forename: F
authors.initials: F
authors.lastname: Salin
authors.forename: R J
authors.initials: RJ
authors.lastname: Petit
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000592:standards; D005819:Genetic Markers; D005820:Genetic Testing / Q000379:methods* / Q000592:standards; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000592:standards; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction / Q000379:methods / Q000592:standards
chemical_list: D005819:Genetic Markers