Targeted Sequencing Applied to High-Throughput Genotyping of the Highly Polyploidy Sugarcane Genome

Sugarcane is an important crop planted worldwide for sugar and biofuel production. Commercial sugarcane cultivars are complex hybrids derived from two species, Saccharum spontaneum and Saccharum officinarum, which contain different number of chromosomes and ploidy. Until now this complexity has delayed the genome characterization and genomics application in breeding, but improvements in methods of sequence-capture and sequencing technologies can now eliminate these obstacles. Here we report the development of a high-throughput genotyping platform for sugarcane based on genome capture followed by next-generation sequencing. As a sugarcane reference genome is not available, the development of hybridization probes relied on a public unigene set and short-read shotgun sequences anchored to the closely related genome of sorghum. Non-repetitive, evenly distributed regions of the sorghum genome were chosen and 40,000 biotinylated probes were designed based on the sugarcane sequences anchored to these positions. Probes were used to capture these regions of the genome on 190 samples from a biparental cross and selfing population, including the parents, and were sequenced on Illumina HiSeq platform. The alignment of the reads to the target regions allowed the identification of 155,427 SNPs in the population, illustrating the high nucleotide diversity of the species. The analysis of samples performed as independent duplicates show a median repeatability of the genotypic call of 97%, suggesting that the approach is viable for large-scale genotyping. Combination of linked SNPs into allelic haplotypes was generated and is being used for mapping in the biparental population and segregation analyzing in the selfed individuals.