Open AccessFast, cost-effective development of species-specific microsatellite markers by genomic sequencing
Author(s) -
Jawad Abdelkrim,
Bruce C. Robertson,
JoAnn L. Stanton,
Neil J. Gemmell
Publication year - 2009
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/000113084
Subject(s) - microsatellite , biology , genetics , dna sequencing , genetic marker , computational biology , genomic library , recombinant dna , genomic dna , genome , population , genomics , organism , gene , base sequence , allele , demography , sociology
Microsatellites are the genetic markers of choice for many population genetic studies, but must be isolated de novo using recombinant approaches where prior genetic data are lacking. Here we utilized high-throughput genomic sequencing technology to produce millions of base pairs of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci. Using this approach we isolated 13 polymorphic microsatellites for the blue duck (Hymenolaimus malacorhynchos), a species for which limited genetic data were available. Our genomic approach eliminates recombinant genetic steps, significantly reducing the time and cost requirements of marker development compared with traditional approaches. While this application of genomic sequencing may seem obvious to many, this study is, to the best of our knowledge, the first attempt to describe the use of genomic sequencing for the development of microsatellite markers in a non-model organism or indeed any organism.