Ultra High Density Mapping of the Saccharum spontaneum Genome

Sugarcane is an important sugar crop contributing up to 80% of the world sugar production. S. spontaneum is one of the three founding species in Saccharum, contributing to hybrid species S. sinense and S. barberi. It provides biotic and abiotic stress tolerance in modern sugarcane hybrid cultivars. AP85-441 is a haploid clone developed from anther culture of octoploid SES208, and has the smallest genome with 32 chromosomes in the genus Saccharum. Pacbio single-molecule real-time (SMRT) sequencing technology was used to sequence this haploid genome at 77X coverage. A mapping population was developed from a cross between double haploid AP83-108 and its pollen source SES208. The genomes of the F1 population was sequenced at 5X coverage using Illumina HiSeq2500. The assembled draft genome of AP85-441 was used as a reference for SNP calling. A total of 1,012,394 and 53,634 high quality single-dose SNP markers were generated, and 29,902 and 13,542 bin markers were subsequently constructed, from SES208 and AP83-108, respectively. These two genetic maps will be used to anchor the haploid genome to 32 chromosomes. The genome composition of the haploid genome AP85-441 and double haploid genome AP83-108 will be revealed by comparison to the octoploid genetic map of SES208.