Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals

• Published in: Molecular ecology resources Vol. 15; no. 1; pp. 17 - 27
• Main Authors: Vukosavljev, M., Esselink, G. D., van 't Westende, W. P. C., Cox, P., Visser, R. G. F., Arens, P., Smulders, M. J. M.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.01.2015; Wiley Subscription Services, Inc
• Subjects: Computational Biology - methods; construction; diversity; est-ssr markers; Gene loci; Genetic markers; Genetic Variation; genetic-linkage maps; Genomics; Genotyping Techniques - methods; identification; in-silico; l; microsatellite marker; Microsatellite Repeats; Molecular Sequence Data; next-generation sequencing; Repetitive Sequences, Nucleic Acid; RNA-seq; Rosa - classification; Rosa - genetics; rose; Sequence Analysis, DNA; simple sequence repeat; Transcriptome; transferability; variability; RNA-seq; microsatellite marker; simple sequence repeat; next-generation sequencing

The first hurdle in developing microsatellite markers, cloning, has been overcome by next‐generation sequencing. The second hurdle is testing to differentiate polymorphic from nonpolymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of al...