Molecular Breeding

, Volume 33, Issue 4, pp 835–849 | Cite as

The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences

  • Joanne Russell
  • Christine Hackett
  • Pete Hedley
  • Hui Liu
  • Linda Milne
  • Micha Bayer
  • David Marshall
  • Linzi Jorgensen
  • Sandra Gordon
  • Rex BrennanEmail author


A genotyping by sequencing (GbS) approach is reported in blackcurrant (Ribes nigrum L.) using a de novo read assembly method developed because of the current absence of a reference genome sequence for this species. A new approach to single nucleotide polymorphism (SNP) genotype calling is described, where individual genotypes for a large number of SNPs were characterised from the GbS counts using a novel method based on a functional regression of major and minor allele read counts. The high-quality GbS SNPs were combined with SNPs and simple sequence repeats generated from other technologies to develop a linkage map with increased marker density and improved genome coverage, containing up to 204 SNPs on each linkage group. SNPs of lower quality were then located on the map using quantitative trait locus (QTL) interval mapping of the proportion of the major allele. Two QTL each for 100-berry weight and Brix scores, measured over three years, were identified using the map. The use of this approach to identify and map a significant number of novel SNPs in a woody species with hitherto limited genomic resources may have generic application to other under-resourced and minor species in the development of cost-effective and efficient high-density genetic maps.


Genotyping by sequencing Ribes Woody perennial SNP discovery Linkage map 



Genotyping by sequencing


Single nucleotide polymorphism


Simple sequence repeat


Amplified fragment length polymorphism


Quantitative trait locus


Second-generation sequencing


Sequencing-based genotyping


Reduced representation libraries


Restriction site associated DNA


100-Berry weight



Support for this work from the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS) and the EU FP7 EUBerry project is gratefully acknowledged.

Supplementary material

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Supplementary material 1 (PDF 74 kb)
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Supplementary material 5 (PDF 185 kb)
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Supplementary material 6 (DOCX 14 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Joanne Russell
    • 1
  • Christine Hackett
    • 2
  • Pete Hedley
    • 1
  • Hui Liu
    • 3
  • Linda Milne
    • 1
  • Micha Bayer
    • 1
  • David Marshall
    • 1
  • Linzi Jorgensen
    • 1
  • Sandra Gordon
    • 1
  • Rex Brennan
    • 1
    Email author
  1. 1.The James Hutton InstituteInvergowrie, DundeeUK
  2. 2.Biomathematics and Statistics ScotlandInvergowrie, DundeeUK
  3. 3.Biomedical Sciences Research ComplexUniversity of St AndrewsFifeUK

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