Just Genes - well mostly: genomic enrichment for sugarcane genic regions

An efficient route to the discovery of polymorphisms in large target regions such as the exome, especially in species with large polyploid genomes, is genomic enrichment. We have used a solution based hybridisation capture method to enrich for genic regions of the sugarcane genome based mainly on the sequence of the related Sorghum genome. Probes designed to Sorghum genes as well as selected regions of sugarcane sequence, were used to capture sequence targeted to genes, followed by identification of single nucleotide polymorphisms (SNPs). This approach was compared with SNP detection in genes from whole genome shotgun (WGS) sequencing for two sugarcane genotypes. The Agilent SureSelect system with approximately 52,400 unique probes was used to capture the sequence from WGS libraries prepared for and previously sequenced with the Illumina Genome Analyser. Ten to eleven fold enrichment was achieved across the selected probes, covering approximately 5.8 Mb of sequence. Reads mapping uniquely to the Sorghum genome provided the basis for SNP detection. The enriched libraries provided a large haul of SNPs within genes with 140,000 SNPs discovered in 13,000 genes for one genotype from one lane of Illumina sequence with the second genotype providing 168,000 SNPs in 15,800 genes. This should enable the mapping of SNPs from practically any gene of choice within the cross of these two sugarcane genotypes. Using this approach the enrichment of genomes is not restricted to species with a complete genome sequence but can be extended to related species.