Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Development And Application Of An Informative Set Of Anchored Markers For Tomato Breeding

Allen Van Deynze¹ , Esther van der Knaap² , David Francis²

¹  Seed Biotechnology Center, University of California, Davis, 95616

²  Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH

This research is intended to bridge a gap between the number of DNA-based markers available for genetic analysis and those that are applicable in breeding populations of tomato. It has been shown that polymorphism for SNPs in tomato is five-fold higher in introns than coding sequences. A Conserved Orthologous Set (COS) of 1500 sequences was used as substrate to design primers across predicted introns in tomato. Primers were prescreened by sequencing a set of three pools of four breeding lines. Polymorphic loci were then amplified and sequenced in 11 individual lines representing processing and fresh market tomato breeding germplasm and L. pimpinellifolium, a close relative. Over 95% of the primers designed span introns and are single copy. About 30% of the loci show putative polymorphisms in pools and 20% are confirmed to be polymorphic in our panel of 11 breeding lines. Intron length in tomato is significantly higher than Arabidopsis. One to seven SNPs are found in polymorphic loci with an average of 2.5 SNPs/locus. Sequences will be made available on Genbank and SGN. The SNPs are being screened in an expanded panel of 48 breeding lines and mapped in populations segregating for fruit shape and quality. Results will be made available in a relational database, www.tomatomap.net. This strategy effectively selects SNP markers that are polymorphic in breeding germplasm and significantly reduces costs in marker discovery.