Genome sequencing for marker discovery in sugarcane

The sequencing of the sugarcane genome to produce a complete assembled sequence will be an important platform for sugarcane research. However, because of the complexity of this genome, assembly of the sequence from the short sequence reads that can now be cost effectively collected remains a significant challenge. Genome sequence may produce more immediate outcomes before complete assembly of the genome is achieved. Deep sequencing of gene rich fractions of the genome from many genotypes will define genetic diversity in sugarcane genes and provide very large numbers of genetic markers. We have obtained random shot gun sequences from the whole genome of several important genotypes and will use those as references to determine the success of genome enrichment systems. The genotype R570 will be used as a source of BAC clones for extensive sequencing of the sugarcane genome. Q165 and IJ76-514 are parents of populations with extensive maps. SP80-3280 is the subject of large scale sequencing. LA purple and Mandalay allow analysis of Saccharum officinarum and S. spontaneum genomes separately.