Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of
Sung-Chur Sim1, Matthew D Robbins, Charles Chilcott
1Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA. sim.16@osu.edu
Background:
Cultivated tomato (Solanum lycopersicum L.) has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP) discovery as a high-throughput approach for marker development in cultivated tomato.
Results:
Three varieties, FL7600 (fresh-market), OH9242 (processing), and PI114490 (cherry) were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (alpha) used to define the confidence interval (CI), and ranged from 76% for polymorphisms identified at alpha
Conclusion:
Array-based SFP discovery was an efficient method to identify a large number of molecular markers for genetics and breeding in elite tomato germplasm. Patterns of sequence variation across five major tomato groups provided insight into to the effect of human selection on genetic variation.
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