Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Diversity Arrays Technology (DArT) For High Throughput, Whole-Genome Molecular Analysis In Sugarcane

Katarzyna Heller-Uszynska¹ , Jason Carling¹ , Margaret Evers¹ , George Piperidis² , Ross Gilmour² , Karen Aitken³ , Philip Jackson³ , Eric Huttner¹ , Andrzej Kilian¹

¹  Diversity Arrays Technology Pty Ltd GPO Box 7141, Yarralumla, ACT 2600, Australia

²  BSES Limited, PMB 57 Mackay Mail Centre Qld 4741 Australia

³  CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia

Several types of molecular markers have been established for this crop including RFLP, SNP, AFLP and SSR. Markers developed so far were used for molecular investigation of sugarcane genome structure, for tracking genetic diversity and genetic/QTL mapping. However, speed and cost of analysis limit the application of current marker technologies for sugarcane molecular breeding, diversity and identity testing.
Diversity Arrays Technology (DArT) combines the ability to identify various types of DNA polymorphism with the low cost and high throughput of the DNA microarray platform (www.DiversityArrays.com). Once established, DArT offers a 10-fold gain over other technologies in terms of marker throughput and assay cost. DArT was effectively developed and delivered in a number of plant species including large genome cereals, wheat and barley. Here we report the successful validation of DArT for sugarcane, one of the most genetically complex crops. We tested eleven methods of genome complexity reduction to determine the most efficient in detecting polymorphism, and therefore offering low cost of data production. Several effective methods of genome complexity reduction were established, including a subtractive method to enrich for polymorphic clones. We then established a detailed protocol for performing DArT in sugarcane. Using the most effective complexity reduction method (PstI/TaqI) over three hundred polymorphic markers were identified. The PstI/TaqI array was then successfully used for diversity analysis of cultivated materials and ancestral lines as well as for mapping the PJ2 cross (Q165 x IJ76-514A). We will present our efforts towards establishing DArT sugarcane arrays capable of typing several thousand markers for molecular breeding and association mapping applications.