Abstract
BackgroundCultivated 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.ResultsA 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.ConclusionSequences 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.
Highlights
Cultivated strawberry (Fragaria × ananassa) represents one of the most valued fruit crops in the United States
In this report we identify over 1300 unique transcripts assembled from 1,847 expressed sequence tags (ESTs) derived from whole-plant vegetative tissues 24 h after salicylic acid treatment
The Fragaria × ananassa EST library The Lambda ZAP cDNA library was generated from whole-plant tissues from mature plants 24 after salicylic acid treatment
Summary
Cultivated strawberry (Fragaria × ananassa) represents one of the most valued fruit crops in the United States. 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. Commercial strawberry has a value of 1.4 billion dollars in the United States, and represents a significant regional crop throughout the world. The information discrepancy is a consequence of limited molecular study in the challenging octoploid cultivated varieties. The thin public informatics base represents a barrier to meaningful study of functional genomics, genetic mechanisms, as well as the (page number not for citation purposes). The dearth of sequence information has limited agile molecular resolution studies in this important crop plant
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