Conservation Genetics Resources

, Volume 8, Issue 2, pp 105–107 | Cite as

Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)

  • Katrin Heer
  • Kristian K. Ullrich
  • Sascha Liepelt
  • Stefan A. Rensing
  • Jiabin Zhou
  • Birgit Ziegenhagen
  • Lars Opgenoorth
Technical Note

Abstract

A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in Germany (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome assembly. This resulted in 111,849 and 366,577 SNPs, respectively. Out of these, 311 were either randomly selected or chosen because of their pronounced divergence between sampling sites and genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.

Keywords

RNA-seq Single nucleotide polymorphism Norway spruce Genotyping 

Supplementary material

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Supplementary material 1 (PDF 64 kb)
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Supplementary material 7 (PDF 228 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Katrin Heer
    • 1
    • 2
  • Kristian K. Ullrich
    • 3
  • Sascha Liepelt
    • 1
  • Stefan A. Rensing
    • 3
  • Jiabin Zhou
    • 2
    • 4
  • Birgit Ziegenhagen
    • 1
  • Lars Opgenoorth
    • 2
  1. 1.Conservation BiologyPhilipps-Universität MarburgMarburgGermany
  2. 2.Department of Ecology, Animal Ecology, Faculty of BiologyPhilipps-Universität MarburgMarburgGermany
  3. 3.Plant Cell BiologyPhilipps-Universität MarburgMarburgGermany
  4. 4.Molecular Ecology Group, State Key Laboratory of Grassland Agro-Ecosystem, College of Life ScienceLanzhou UniversityLanzhouChina

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