Target Sequencing Reveals Natural Allelic Variation in Saccharum Complex

Sugarcane (Saccharum spp.) is an important sugar and biofuel crop characterized by highly polyploid and complex genomes. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic sequence variations and dissecting alleles and allele variant recombination controlling species adaptation and important agronomical traits. To characterize natural allelic variance in the “Saccharum complex”, a target enrichment approach followed by deep sequencing was applied to 12 representative germplasm accessions. In total, 55,946 probes were designed from sorghum genome and sugarcane unigene set targeting 6.7 Mb of the sugarcane genome. A pipeline for polyploidy sequence variance and genotype calling was established. A total of 1,112,915 non-redundant single nucleotide polymorphisms (SNPs), 19,354 InDels, 1,021 gene copy number variations, and 3,086 gene presence/absence variants were detected among the 12 accessions. The genotypes based on the SNP loci of each accession and their ploidy levels were estimated as largely homozygote. A total of 13,584 haplotype blocks were inferred according to 406 candidate genes. The synonymous and non-synonymous substitution rates analysis revealed that the highest divergence time among the Saccharum spp. was 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum, the two close genera of Saccharum, approximately 5 and 6 MYA, respectively. The results demonstrated that hybridization-based target enrichment sequencing approach provided an effective way to discover natural allelic variation in highly polyploid species. The catalog of sequence variants among different genotypes in “Saccharum complex” will facilitate further gene/trait association studies for polyploidy sugarcane improvement.