Pumpkin ( Cucurbita spp.) is one of the major vegetable crops grown worldwide. The number of simple sequence repeat (SSR) markers in pumpkins lags far behind the requirement of genetic analysis. Transcriptomes generated from different genotypes provide valuable sequence resources for molecular marker development. In this study, transcriptomes from the roots of C. maxima and C. moschata inbred lines suffering salinity stress were separately de novo assembled. The assembled unigenes were aligned between the two genotypes to in silico screen the polymorphic SSR loci. A total of 328 putatively polymorphic SSR loci were identified. Of which, 211 loci that is suitable to the primer design were selected for polymorphic validation by polymerase chain reaction amplification and electrophoresis analysis. A total of 110 SSR markers exhibited polymorphism among 65 pumpkin varieties with the mean polymorphism information content value of 0.34. Cluster analysis showed that these SSR markers distinctly classified the pumpkin varieties into different groups according to their genetic backgrounds at species level. The SSR markers developed in this study provided valuable supplements to the available genetic tools of pumpkins.

中文翻译：

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从从头组装的南瓜转录组中开发简单序列重复标记

南瓜（Cucurbita spp.）是世界范围内种植的主要蔬菜作物之一。南瓜中简单序列重复（SSR）标记的数量远远落后于遗传分析的要求。从不同基因型产生的转录组为分子标记开发提供了宝贵的序列资源。在这项研究中，来自遭受盐分胁迫的 C. maxima 和 C. moschata 自交系根的转录组分别从头组装。组装的 unigenes 在两种基因型之间对齐，以在 silico 筛选多态性 SSR 基因座。总共确定了 328 个假定的多态性 SSR 基因座。其中，选择适合引物设计的211个位点，通过聚合酶链反应扩增和电泳分析进行多态性验证。共有110个SSR标记在65个南瓜品种中表现出多态性，平均多态性信息含量值为0.34。聚类分析表明，这些 SSR 标记根据其在物种水平上的遗传背景将南瓜品种明显地分为不同的组。本研究中开发的 SSR 标记为可用的南瓜遗传工具提供了宝贵的补充。