Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: SNP
            

DISCOVERY, MAPPING AND APPLICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN LYCOPERSICON ESCULENTUM

¹ Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691

² Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691

³ Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691

Single nucleotide polymorphisms (SNPs) are useful for characterizing allelic variation, for genome-wide mapping, and as a tool for marker-assisted selection. SNP discovery through de novo sequencing is inefficient within cultivated tomato (Lycopersicon esculentum Mill.) because the polymorphism rate is ten-fold lower than the sequencing error rate. It is necessary to sequence up to 80 amplified fragments before discovering a single SNP. The availability of expressed sequence tag (EST) data has made it feasible to discover putative SNPs in silico prior to experimental verification. The tomato genome project has produced 138,100 ESTs (LeGI Release 8.0) derived from libraries of different tissues and varieties. By dividing the tomato ESTs by variety of origin, selecting contigs with a minimum of three sequences to correct for sequence error, and comparing sequences from different varieties, we have identified candidate SNPs for use within cultivated germplasm pools. 1245 contigs having three EST sequences of Rio Grande and three EST sequences of TA496 were used for SNP discovery. We detected 1 SNP for every 7,000 bases analyzed, with 101 candidate SNPs in 31 genes identified. Sixty-six SNPs could be recognized by available restriction enzymes, and subsequent experimental verification using restriction digestion or Cel 1 digestion confirmed 81% of the putative polymorphisms tested. SNPs between Rio Grande and TA496 have a high probability (63%) of detecting SNPs between other L. esculentum varieties. Verification of the remaining candidate SNPs using Cel 1, mapping relative to the RFLP framework map, and application of these SNPs are on going.