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首页> 外文期刊>BMC Plant Biology >Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)
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Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa)

机译：表达八倍体草莓（Fragaria×ananassa）的表达序列标签（EST）和简单的序列重复（SSR）标记

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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.
机译：背景栽培草莓（Fragaria×ananassa）代表美国最有价值的水果作物之一。尽管其经济重视，但八倍体基因组呈现出对基因组结构的有效研究和基本上相关性状的分子机制的突然研究。许多潜在的富有成效的研究途径，特别是大规模的基因表达调查和分子遗传标记的发展已经受到公共数据库中缺乏序列信息的限制。作为补救这种差异的第一步，已经从水杨酸盐处理，整个植物组织和超过1800种表达序列标签（EST）中出现了cDNA文库。结果推出的UNIGENE组1304序列 - 133 CONTIGS和1171个单曲 - 已经开发出来，并且转录物已经在功能上注释。同源性搜索表明，89.5％的序列与已知/推定蛋白质或蔷薇科学股份共享显着的相似性。已经确定了EST的特征表征，并且已经确定了与经济重要性的特定生理过程相关的基因。提出了一组用于SSR开发和映射的工具。结论源自该努力的序列可用于速度在Frantaria和Rosaceae中的基因发现努力，以及比较映射的途径。该报告代表了扩展草莓中分子遗传分析的第一步，并演示了计算工具如何使用来自相对较小的数据集来最佳地挖掘大量有用信息。

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