Skim Based Genotyping by Sequencing in Complex Crop Genomes

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 applied a skim sequencing based approach to genotype the large and complex genomes of Brassica and bread wheat.

First, Illumina whole genome re-sequencing paired reads are mapped to a reference, and SNPs are predicted using our pipeline SGSautoSNP. Next, low coverage genome wide sequencing of individuals is performed and reads mapped to the reference to genotype the previously predicted SNP positions. Missing 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. The genotype data can be applied for genome-wide association studies to link SNPs to certain phenotypes, to infer Linkage Disequilibrium blocks, to find areas of selection based on SNP density, to characterise variation in genome structures or to use in plant-breeding.