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


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.


RNA-seq Single nucleotide polymorphism Norway spruce Genotyping 



We thank the Bavarian Forest National Park for funding the RNA-seq data. KH was funded by the ERAnet BiodivERsA project ‘TipTree’ (ANR-12-EBID-0003) funded by the German Federal Ministry of Education and Research (Grant 01LC1202A). Thanks to M Bacht und C Scherer (University of Marburg) for assistance with RNA extraction and to EM Sehr, M Stierschneider, E Wischnitzki and S Fluch (AIT) for coordinating the SNP genotyping. We thank the Team from and to host the phase corrected GFF file.

Supplementary material

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Supplementary material 1 (PDF 64 kb)
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  1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300Google Scholar
  2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. doi: 10.1093/bioinformatics/btu170 PubMedPubMedCentralGoogle Scholar
  3. Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinform 10:421. doi: 10.1186/1471-2105-10-421 CrossRefGoogle Scholar
  4. Chen J, Källman T, Gyllenstrand N, Lascoux M (2010) New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict. Heredity 104:3–14. doi: 10.1038/hdy.2009.88 CrossRefPubMedGoogle Scholar
  5. Chen J, Källman T, Ma X et al (2012a) Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies). Genetics 191:865–881. doi: 10.1534/genetics.112.140749 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Chen J, Uebbing S, Gyllenstrand N et al (2012b) Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genom 13:589. doi: 10.1186/1471-2164-13-589 CrossRefGoogle Scholar
  7. De Wit P, Pespeni MH, Ladner JT et al (2012) The simple fool’s guide to population genomics via RNA-seq: an introduction to high-throughput sequencing data analysis. Mol Ecol Resour 12:1058–1067. doi: 10.1111/1755-0998.12003 CrossRefPubMedGoogle Scholar
  8. Grabherr MG, Haas BJ, Yassour M et al (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29:644–652. doi: 10.1038/nbt.1883 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Guillet-Claude C, Isabel N, Pelgas B, Bousquet J (2004) The evolutionary implications of knox-I gene duplications in conifers: correlated evidence from phylogeny, gene mapping, and analysis of functional divergence. Mol Biol Evol 21:2232–2245. doi: 10.1093/molbev/msh235 CrossRefPubMedGoogle Scholar
  10. Heuertz M, De Paoli E, Källman T et al (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174:2095–2105. doi: 10.1534/genetics.106.065102 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Källman T, De Mita S, Larsson H et al (2014) Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst.]. PLoS One 9:e95306CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kim D, Pertea G, Trapnell C et al (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36. doi: 10.1186/gb-2013-14-4-r36 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25CrossRefPubMedPubMedCentralGoogle Scholar
  14. Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. doi: 10.1093/bioinformatics/btr509 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Lind M, Källman T, Chen J et al (2014) A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One 9:e101049. doi: 10.1371/journal.pone.0101049 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Nystedt B, Street NR, Wetterbom A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497(7451):579–584. doi: 10.1038/nature12211 CrossRefPubMedGoogle Scholar
  17. Opgenoorth L (2009) Identification and characterization of microsatellite marker in the tetraploid Juniperus tibetica Kom. using next generation sequencing. Conserv Genet Resour 1:253–255. doi: 10.1007/s12686-009-9062-3 CrossRefGoogle Scholar
  18. Pavy N, Gagnon F, Rigault P et al (2013) Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Mol Ecol Resour 13:324–336. doi: 10.1111/1755-0998.12062 CrossRefPubMedGoogle Scholar
  19. Sundell D, Mannapperuma C, Netotea S et al (2015) The plant genome integrative explorer resource: New Phytol 208:1149–1156. doi: 10.1111/nph.13557 CrossRefPubMedGoogle Scholar

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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