Update on the Sugarcane Genome Sequence

Sugarcane has a complex polyploid hybrid genome of 10 Gbp which makes sequencing the genome a challenge. We present here the Australian contribution to the R570 sugarcane genome sequence. A BAC by BAC sequencing approach is being used to generate a mosaic monoploid genome. We present data on sequence generated from over 1000 R570 BAC clones, these were selected using a number of approaches and were in part targeted to important QTL identified in Australian germplasm. In a parallel approach, we have also generated large amounts of whole genome shotgun (WGS) sequence from variety R570 and used advanced computational methods to assemble this sequence into a number of scaffolds. This WGS data was generated from a range of DNA fragment sizes between 180 bp and 32,000 bp, which should enable even complex regions of the genome to be ordered. In addition to this PacBio long read technology has been used to generate 31.7 Gbp of data with an average read length of 7282 bp. This has been used to help resolve repeats and increase scaffold lengths. In total the data covers the complete genome sequence to a level of 73-fold, representing roughly 1000-fold monoploid genome coverage, which highlights sequence variation at each locus. We present here the analysis of the multiple alleles of genes that are present in the polyploid genome of sugarcane. Analysis of this data has identified large numbers of single nucleotide polymorphisms (SNPs), which are currently being tested for association with desirable traits amongst a population of plant lines. A defined genome sequence will be used by many researchers to identify the basis of traits and to capitalise on knowledge of traits from related crops such as sorghum. Previous work has identified quantitative trait loci (QTL) for traits such as biomass in sugarcane. Bioinformatic tools can now identify the underlying gene sequences from the sugarcane genome sequence. In a similar way, the sugarcane homologues of genes that are known to enhance productivity in other species can now be identified. In addition to revealing underlying biological mechanisms, these genes will be valuable as targets for selection or genetic modification to enhance variety development.