Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)

  • Carolina Bernhardsson
  • Xi Wang
  • Helena Eklöf
  • Pär K. IngvarssonEmail author
Part of the Compendium of Plant Genomes book series (CPG)


Advances in next-generation sequencing methods and the development of new statistical and computational methods have opened up possibilities for large-scale, high-quality genotyping in most organisms. Conifer genomes are large and are known to contain a high fraction of repetitive elements and this complex genome structure has bearings for approaches that aim to use next-generation sequencing methods for genotyping. In this chapter, we provide a detailed description of a workflow for variant calling using next-generation sequencing in Norway spruce (Picea abies). The workflow starts with raw sequencing reads and proceeds through read mapping to variant calling and variant filtering. We illustrate the pipeline using data derived from both whole-genome resequencing data and reduced representation sequencing. We highlight possible problems and pitfalls of using next-generation sequencing data for genotyping stemming from the complex genome structure of conifers and how those issues can be mitigated or eliminated.


Genotyping Next-generation sequencing Norway spruce Variant calling Variant filtering 


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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Carolina Bernhardsson
    • 1
    • 2
  • Xi Wang
    • 1
    • 2
  • Helena Eklöf
    • 1
  • Pär K. Ingvarsson
    • 1
    Email author
  1. 1.Department of Plant BiologyLinnean Centre for Plant Biology, Swedish University of Agricultural SciencesUppsalaSweden
  2. 2.Department of Ecology and Environmental ScienceUmeå Plant Science Centre, Umeå UniversityUmeåSweden

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