Open Access Highly Accessed Research article

Diversity in conserved genes in tomato

Allen Van Deynze1*, Kevin Stoffel1, C Robin Buell23, Alexander Kozik4, Jia Liu2, Esther van der Knaap5 and David Francis5

Author Affiliations

1 Seed Biotechnology Center, University of California, 1 Shields Ave., Davis, CA, USA

2 The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD, USA

3 Department of Plant Biology, Michigan State University, 166 Plant Biology, East Lansing, MI, USA

4 Genome and Biomedical Sciences Facility, University of California, 1 Shields Ave., Davis, CA, USA

5 Department of Horticulture and Crop Science, The Ohio State University/OARDC, 1680 Madison Ave, Wooster, OH, USA

For all author emails, please log on.

BMC Genomics 2007, 8:465  doi:10.1186/1471-2164-8-465

Published: 18 December 2007



Tomato has excellent genetic and genomic resources including a broad set of Expressed Sequence Tag (EST) data and high-density genetic maps. In addition, emerging physical maps and bacterial artificial clone sequence data serve as template to investigate genetic variation within the cultivated germplasm pool with the goal to manipulate agriculturally important traits. Unfortunately, the nearly exclusive focus of resource development on interspecific populations for genetic analyses and diversity studies has left a void in our understanding of genotypic variation within tomato breeding programs that focus on intra-specific populations. We describe the results of a study to identify nucleotide variation within tomato breeding germplasm and mapping parents for a set of conserved single-copy ESTs that are orthologous between tomato and Arabidopsis.


Using a pooled sequencing strategy, 967 tomato transcripts were screened for polymorphism in 12 tomato lines. Although intron position was conserved, intron lengths were 2-fold larger in tomato than in Arabidopsis. A total of 1,487 single nucleotide polymorphisms and 282 insertion/deletions were identified, of which 579 and 206 were polymorphic in breeding germplasm, respectively. Fresh market and processing germplasm were clearly divergent, as were Solanum lycopersicum var. cerasiformae and Solanum pimpinellifolium, tomato's closest relatives. The polymorphisms identified serve as marker resources for tomato. The COS is also applicable to other Solanaceae crops.


The results from this research enabled significant progress towards bridging the gap between genetic and genomic resources developed for populations derived from wide crosses and those applicable to intra-specific crosses for breeding in tomato.