Skip to main content
Log in

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

We characterise the distribution of crossover and non-crossover recombination in Brassica napus and Cicer arietinum using a low-coverage genotyping by sequencing pipeline SkimGBS.

Abstract

The growth of next-generation DNA sequencing technologies has led to a rapid increase in sequence-based genotyping for applications including diversity assessment, genome structure validation and gene–trait association. We have established a skim-based genotyping by sequencing method for crop plants and applied this approach to genotype-segregating populations of Brassica napus and Cicer arietinum. Comparison of progeny genotypes with those of the parental individuals allowed the identification of crossover and non-crossover (gene conversion) events. Our results identify the positions of recombination events with high resolution, permitting the mapping and frequency assessment of recombination in segregating populations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

Download references

Acknowledgments

The authors would like to acknowledge funding support from the Australian Research Council (Projects LP0882095, LP0883462, LP110100200 and DP0985953), the Australian India Strategic Research Fund (AISRF) Grand Challenge fund (GCF010013), CGIAR Generation Challenge Programme (Theme Leader Discretionary grant), the Australian Genome Research Facility (AGRF), the Queensland Cyber Infrastructure Foundation (QCIF) and the Australian Partnership for Advanced Computing (APAC) and the Center of Excellence in Genomics (CEG) of ICRISAT. The part of this work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.

Conflict of interest

The authors declare no conflict of interest.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to David Edwards.

Additional information

Communicated by L. Jiang.

All scripts used in this study are available at http://www.appliedbioinformatics.com.au/index.php/SkimGBS.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 1715 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bayer, P.E., Ruperao, P., Mason, A.S. et al. High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus . Theor Appl Genet 128, 1039–1047 (2015). https://doi.org/10.1007/s00122-015-2488-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-015-2488-y

Keywords

Navigation