History and Development of Molecular Markers for Sugarcane Breeding

Sugarcane ( Saccharum spp. hybrids) is one of the world’s most important economic crops for both the food and biofuel industries. It has one of the most complex genomes of any crop plant, varieties are unbalanced polyploids and derived from interspecific hybridisation between the domesticated Saccharum officinarum and a wild relative S. spontaneum . Here I review sugarcane’s complex genetics and chart the history of DNA marker development in sugarcane over the last 30 years. Despite its complex autopolyploid genome of over 100 chromosomes, marker development has spanned the first hybridisation-based markers, restriction fragment length polymorphism markers (RFLP) to the high-throughput next generation sequence methods currently used to detect single nucleotide polymorphism (SNP). Although there is a long history of research and development in sugarcane, it is only comparatively recently that marker technology has caught up with the need for discovery of large numbers of single-dose SNP markers and methods for genotyping that are fast, efficient and cost-effective that can be used for selection in a breeding program. The choice of genotyping platform depends on the breeding application and both whole genome SNP methods (array-based and genotype-by-sequencing (GBS)) and low density scalable and cost-effective platform technologies have a place in sugarcane breeding.