Single Nucleotide Polymorphism (SNP) Discovery in the Large and Complex Saccharum Spp. Genomes through Exome Sequencing

Sugarcane (Saccharum spp.), as one of the important sugar and biofuel crops, is a highly polyploid and mostly aneuploid. DNA polymorphism discovery, especially for the genome-wide SNP discovery remains challenging in sugarcane due to high level of genome complexity. Advancement of next generation sequencing (NGS) technologies and the approval of genome enrichment approaches have largely enabled high throughput SNP discovery in sugarcane. In this study, we have applied targeted-capture sequencing of 12 sugarcane genotypes representing nine different species to identify genomic composition and allelic diversity in sugarcane. Chromosome number of the 12 genotypes estimated by flow cytometry ranged from 48 to 115, which facilitated the allelic dosage estimation in each sugarcane genotype. For exome capture, 55,946 120-mer probes were designed based on sugarcane and sorghum transcript sequences. The captured regions of sugarcane genomes were deep-sequenced. A total of 411 million reads from 12 genotypes were generated representing nearly 53 times coverage of the sugarcane exome sequences. Approximately 115 thousands SNPs were discovered with the genome of sorghum as reference. Among all the SNPs, 8,069 (3.3%) were identified as non-synonymous and 33,032 (91.1%) were in gene regions. These SNPs were dispersed across the entire genome in consistence with the distribution of probes. The overall estimated SNP variant rate was one per 5,723 bases and the ratio of transition to transversion was 2.01. This high-density SNP provides a valuable resource for defining genotype variation across the genome, and as a great tool for traits mapping and marker assisted breeding.