Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology.
The dwarf bulrush (Typha minima Funck ex Hoppe) is an endangered pioneer plant species of riparian flood plains. In Switzerland, only 3 natural populations remain, but reintroductions are planned. To identify suitable source populations for reintroductions, we developed 17 polymorphic microsatellite markers with perfect repeats using the 454 pyrosequencing technique and tested them on 20 individuals with low-cost M13 labeling. We detected 2 to 7 alleles per locus and found expected and observed heterozygosities of 0.05-0.76 and 0.07-1, respectively. The whole process was finished in less than 6 weeks and cost approximately USD 5000. Due to low costs and reduced expenditure of time, the use of next-generation sequencing techniques for microsatellite development represent a powerful tool for population genetic studies in nonmodel species, as we show in this first application of the approach to a plant species of conservation importance.
Csencsics
Daniela
D
Research Unit Ecological Genetics and Evolution, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland. daniela.csencsics@wsl.ch
Brodbeck
Sabine
S
Holderegger
Rolf
R
D000483:Alleles; D001483:Base Sequence; D003362:Cost-Benefit Analysis; D017931:DNA Primers; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics; D056727:Endangered Species; D056426:Genetic Loci; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000191:economics; D013045:Species Specificity; D013557:Switzerland; D032401:Typhaceae / Q000235:genetics*
D017931:DNA Primers; D018744:DNA, Plant