Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing

被引:262
作者
Abdelkrim, Jawad [1 ,2 ]
Robertson, Bruce C. [2 ,3 ]
Stanton, Jo-Ann L. [4 ]
Gemmell, Neil J. [1 ,2 ]
机构
[1] Univ Otago, Dept Anat & Struct Biol, Ctr Reprod & Genom, Dunedin 9054, New Zealand
[2] Univ Canterbury, Sch Biol Sci, Christchurch 1, New Zealand
[3] Univ Otago, Dept Zool, Dunedin 9054, New Zealand
[4] Univ Otago, Dept Anat & Struct Biol, Anat Otago Genom Sequencer Unit, Dunedin 9054, New Zealand
关键词
microsatellites; genomics; high-throughput sequencing; Hymenolaimus malacorhynchos; conservation biology;
D O I
10.2144/000113084
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:185 / +
页数:5
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