DArT Markers for Linkage Mapping and Cross-Species Comparison of Genome Structures

Diversity Arrays Technology (DArT) provides a high throughput, microarray-based marker platform for analysis of plant genomes. The technology is particularly well adapted to cross-species comparative applications. In collaboration with Diversity Arrays Technology, Pty. Ltd., we have developed a DArT array for use with wild Solanum species of breeding potential for potato improvement. Comprised of approximately 16,000 elements, the current DArT array is optimized for study of the potato tertiary genepool, a group of about 18 disease, pest, and stress tolerant species. To date, DArT-linkage maps have been constructed for two species: S. bulbocastanum and S. commersonii. DArT markers correspond to bacterial clone libraries. Plasmid inserts for more than 500 DArT markers mapped in S. bulbocastanum were sequenced. The resulting sequences were aligned to burgeoning tomato and potato whole genome sequences, facilitating comparison of genome structures between tomato, potato, and S. bulbocastanum. This analysis allowed assignment of S. bulbocastanum linkage groups to specific tomato and potato chromosomes and validates map development procedures for S. bulbocastanum. Results to date reveal nearly perfect conservation of marker order across the three species and within each genetic linkage group.  However, marker order is disrupted by a limited number of large-scale chromosome rearrangements (e.g. inversions and translocations) associated with species divergence. Our analyses suggest that the genome of S. bulbocastanum is more similar in structure to that of potato than tomato, consistent with reported phylogenetic relationships. Additionally, we are evaluating the relationships between physical and genetic distances across species on a genome-wide scale. Understanding similarities and differences in genome structure has implications for the use of wild relatives of crop plants in breeding and gene mapping/cloning. This project was supported by the National Research Initiative of USDA’s National Institute of Food and Agriculture.