Genome Assembly Validation and Trait Association using Skim Based Genotyping by Sequencing in Canola

Several methods have been developed for genotyping by sequencing using next generation DNA sequencing technology. These often include complexity reduction steps to reduce the cost of data generation. As an alternative to complexity reduction, we have developed and applied a skim sequencing based approach to genotype canola (Brassica napus) at a very high resolution.

First, Illumina whole genome re-sequencing data from the parents of a mapping population are aligned with a reference genome and SNPs are predicted using SGSAutoSNP. Next, low coverage genome wide skim sequencing of the population is performed and reads mapped to the reference to genotype the previously predicted SNPs. Missing SNP positions are imputed using known haplotype block information, and recombination positions predicted. An advantage of this approach is that additional sequence data can be generated from select individuals to increase the genotyping resolution.

This approach offers a fast, easy and flexible way to genotype large numbers of SNPs across populations. This genotype data can be applied for genome-wide association studies, to characterise recombination, and assess structural variation or errors in genome assemblies.