Can genomics revolutionise genetics and breeding in sugarcane?

Sugarcane has the most complex genome of any crop plant. Commercial sugarcane cultivars are the result of a limited series of crosses and backcrosses derived from two Saccharum species and are poly-aneuploid hybrids with chromosome numbers in excess of 100. Almost all traits are quantitatively inherited and genetic mapping is mainly restricted to dominant single dose DNA markers. In 2003, enormous amounts of DNA sequence information became available via the release of 255,000 expressed sequence tags for sugarcane. It is now possible to identify candidate gene sequences that may underpin important traits in sugarcane and to characterise single nucleotide polymorphisms (SNPs) in these genes. Combinations of SNPs in a gene sequence act as signatures for individual gene haplotypes that may be considered as allele equivalents in the sugarcane genome. Techniques for reliably measuring the dosage of SNPs in the sugarcane genome have emerged and can be used to provide information that enables the gene haplotype (allele) content in a sugarcane genotype to be deduced. This paper describes how these genomics-based tools provide new strategies for genetic analysis and plant improvement in sugarcane.