Plant & Animal Genomes XIV Conference

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

Computational Mapping Of Crop Plant ESTs

Thomas Thiel^1,3 , Andreas Graner¹ , Stefan Posch^2,3 , Nils Stein¹ , Rajeev K. Varshney¹ , Ivo Grosse^1,3

¹  Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, D-06466, Germany

²  Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle (Saale), D-06120, Germany

³  Bioinformatics Center Gatersleben-Halle (BIC-GH), Corrensstrasse 3, Gatersleben, D-06466, Germany

The genetic mapping of Expressed Sequence Tags of crop plants is a fundamental step for many molecular applications. However, this process is time consuming, costly, labour intensive, and depends on the presence of DNA polymorphisms within mapping populations. One computational approach to address this problem uses a relatively small number of experimentally mapped ESTs together with the genomic sequence of a suitable model plant and involves the following three steps: (1) spliced alignment of the ESTs with the genomic DNA of a completely sequenced model plant using spliced alignment programs, such as Sim4, Spidey, GeneSeqer, and Blat, (2) Detection of syntenic regions characterized by a colinear order of genes using the mapping location of an adequate number of ESTs, and (3) Prediction of the mapping positions of the remaining ESTs based on the established colinearity model. Using the example of barley and rice, we show that the seven barley and twelve rice chromosomes share large syntenic regions despite both species diverged more than 60 million years ago. We use the IPK barley transcript map, which currently consists of about 1,000 experimentally mapped ESTs to establish a barley-rice colinearity model, and we apply this model to predict the genetic mapping positions of a large portion of the approximately 400,000 publicly available barley ESTs.