High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus
- 1.4k Downloads
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.
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.
KeywordsRecombination Event Gene Conversion Genome Sequence Data Cicer Arietinum Gene Conversion Event
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.
- Wijnker E et al. (2013) The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. Elife 2: e01426 doi: 10.7554/eLife.01426