Journal
PLANT MOLECULAR BIOLOGY REPORTER
Volume 28, Issue 2, Pages 352-356Publisher
SPRINGER
DOI: 10.1007/s11105-009-0154-8
Keywords
Bioinformatic tool; Sequence analysis; Gene annotation; Biological database; Functional marker development
Categories
Funding
- Center for Plant Molecular Genetics and Breeding Research
- Crop Functional Genomics Center
- Plant Diversity Resource Center
- Ministry of Education, Science and Technology
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A simple sequence repeat-functional domain marker (SSR-FDM) relies on development of molecular markers for putative functional domains using simple sequence repeats and in silico annotated information of those sequences using biological databases. A total of 148,921 tomato ESTs and 115,598 pepper ESTs were analyzed, resulting in the identification of 439 tomato SSR-FDMs and 489 pepper SSR-FDMs. Among them, 54 pepper SSR-FDMs were tested on pepper. Several genomic databases were used for the in silico annotation of the SSR-FDM sequences that revealed a wide range of candidate genes. This study demonstrates that SSR-FDMs provide information regarding transcribed genetic markers and putative function as a genomic resource database for Solanaceae. This system could be applied to the development of a functional marker database for any crop species.
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