Plant & Animal Genomes XV Conference

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

Gene Pair Markers: An Innovative Tool For Comparative Linkage Mapping In The Rosaceae Family And In Other Taxa With Small Genomes

Thomas M. Davis¹ , M. E. Shields¹ , Qian Zhang¹ , Denise Tombolato² , Kevin M. Folta²

¹  Department of Plant Biology, University of New Hampshire, Rudman Hall, Durham, NH, 03824, USA

²  Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, PO Box 110690, 1301 Fifield Hall, Gainesville, FL, 32611, USA

Given the relatively small (200 Mb) genome size of the strawberry diploid model species, Fragaria vesca, it is not surprising that genes are closely spaced: about 1 gene per 6 kb. As a consequence of the resultantly small intergenic distances, PCR primers targeted to conserved exon sequences in two adjacent genes (referred to here as a "gene pair") can be used to amplify a product that contains an entire intergenic region flanked by gene-defining exon sequences. Such intergenic regions are rich sites of useful polymorphisms, including SNPs, indels and SSRs. The gene pair marker approach exploits this abundant polymorphism to achieve convenient differentiation between mapping parents, and genotyping of segregating populations, using the CAPS (cleaved amplified polymorphic site) technique - i.e., by restriction enzyme digestion of PCR products followed by visualization on an ethidium bromide stained electrophoretic gel. We are developing gene pair primer sets at about 50 sites broadly distributed across the basic (x=7) strawberry genome, with the expectation of cross-species marker transferability. Using comparison of strawberry exon sequences to homologous EST sequences from other rosaceous species (e.g. cherry, rose, raspberry, apple), we are designing sets of species-specific, or when possible universal, PCR primer pairs that will enable amplification of gene pair loci in multiple rosaceous species. We expect that gene pair markers will constitute a useful new tool for comparative linkage mapping in the Rosaceae family, and that this approach could also be applied in other taxa featuring small genomes with commensurately short intergenic distances.