Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)
| Autor: | Sook Jung, Philip J. Stewart, Margaret Staton, Christopher Jesdurai, Dorrie Main, Dawn Bies, Kevin M. Folta |
|---|---|
| Rok vydání: | 2005 |
| Předmět: |
Genetic Markers
0106 biological sciences Sequence analysis UniGene Plant Science Computational biology Biology Genes Plant Fragaria 01 natural sciences Genome Polyploidy 03 medical and health sciences Sequence Homology Nucleic Acid lcsh:Botany Genomic library Rosaceae Gene Gene Library 030304 developmental biology Expressed Sequence Tags 2. Zero hunger Genetics 0303 health sciences Expressed sequence tag Chromosome Mapping Computational Biology food and beverages Sequence Analysis DNA Plants Genetically Modified lcsh:QK1-989 RNA Plant Genetic marker Microsatellite Repeats Research Article 010606 plant biology & botany |
| Zdroj: | BMC Plant Biology, Vol 5, Iss 1, p 12 (2005) BMC Plant Biology |
| ISSN: | 1471-2229 |
| DOI: | 10.1186/1471-2229-5-12 |
| Popis: | Background Cultivated strawberry (Fragaria × ananassa) represents one of the most valued fruit crops in the United States. Despite its economic importance, the octoploid genome presents a formidable barrier to efficient study of genome structure and molecular mechanisms that underlie agriculturally-relevant traits. Many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases. As a first step to remedy this discrepancy a cDNA library has been developed from salicylate-treated, whole-plant tissues and over 1800 expressed sequence tags (EST's) have been sequenced and analyzed. Results A putative unigene set of 1304 sequences – 133 contigs and 1171 singlets – has been developed, and the transcripts have been functionally annotated. Homology searches indicate that 89.5% of sequences share significant similarity to known/putative proteins or Rosaceae ESTs. The ESTs have been functionally characterized and genes relevant to specific physiological processes of economic importance have been identified. A set of tools useful for SSR development and mapping is presented. Conclusion Sequences derived from this effort may be used to speed gene discovery efforts in Fragaria and the Rosaceae in general and also open avenues of comparative mapping. This report represents a first step in expanding molecular-genetic analyses in strawberry and demonstrates how computational tools can be used to optimally mine a large body of useful information from a relatively small data set. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|