| Abstract Detail
Translational Genomics - Morning Paik, Hyojung [1], Han, Jung-Heon [2], Kim, Byung-Dong [2], Choi, Doil [3], Hur, Chul-Goo [3]. Integrated computational screening of simple sequence repeats (SSRs) coupled with functional domain markers in pepper and tomato expressed sequence tags (ESTs). MARKER Assisted Selection (MAS) strategy has been a big-trend in conventional breeding and positional cloning. High-throughput marker identification is critical requirement for successful MAS approach, while the markers should be evenly distributed in chromosomes as possible. Generally characterization of the gene or the target trait identified makes the research time longer. However some target trait and/or gene identification must be completed in a short period. For instance, the identification of virus resistance trait should be done faster than viral genome evolution. For these reasons, we suggest a new marker system that is based on the distance measure between simple sequence repeat(SSR)and Functional Domain. Our method also integrates every FDM with cDNA microarray data to reduce the research time of functional characterization. We collected 115,598 pepper ESTs and 191,890 tomato ESTs from dbEST. Using these EST sets, the number of 18,431 and 20,396 consensus sequences were generated by StackPACK in pepper and tomato respectively. Functional Domain (FDM) regions are analyzed with InterProScan and SSRs are positioned by RepeatMasker. Our SSR-FDM system principally uses the couple of SSR and FDM, to make a PCR primer set. To improve the efficiency of F2 screening marker selection, we located the probable intronic region between SSR and FDM in every SSR-FDM couple computationally because polymorphism is more frequently occurred in intron than exon. In addition, every SSR-FDMs were combined with the microarray expression data, which were performed in the various conditions of abiotic and biotic stresses. Our SSR-FDM makes it possible to develop markers at fast, the most important prerequisite in MAS and positional cloning. Previously, it was not easy to study characterization of each target traits or genes, by only depending on phenotypic and physical information. However, using our method, almost simultaneous functional characterization is possible after MAS and other positional cloning research.
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Related Links:
pepper and other Solanaceae sequence DB in KRIBB
1 - Korea Research Insititute of Bioscience and Biotechnology, Plant genomic center, Eoun-dong Youseong-gu, Daejeon, 305-333, Korea
2 - Seoul National University, Center for Plant Molecular Genetics and Breeding Research, Horticulture, Sinrim-dong, Seoul, 151-742, Korea
3 - Korea Research Institute of Bioscience and Biotechnology, Plant Genomics Lab, P.O. Box. 115, Taejon, 305-600, South Korea
Keywords:
Marker-Assisted Selection
simple sequence repeat
Pepper
tomato
Functional domain
Bioinformatics.
Session: SAT05-10
Location: Hall of Ideas Room I/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 11:35 AM
Abstract ID:323 |
