Nucleic Acids Res:农科院油料所张秀荣研究组创建植物微卫星DNA发掘
近日，国际核酸类重要学术期刊《Nucleic Acids Research》杂志在线发表了中国农业科学院油料所芝麻与特色油料遗传育种创新团队张秀荣研究员的一篇研究论文，研究论文报道了植物微卫星DNA及其标记开发数据库PMDBase。该数据库的创建和共享将为全球作物功能基因组学和分子育种研究提供全面的、便利的基础平台。于景印博士为论文第一作者，张秀荣研究员为论文通讯作者。
微卫星DNA，也称为SSR，是涉及许多重要生物功能的基因组成分，已被广泛地应用于作物基础研究，包括遗传多样性、连锁和关联作图、标记辅助选择、品种鉴定和进化分析等。
据介绍，该团队开发了一套便捷高效的微卫星DNA位点鉴定及分子标记开发流程，对截至目前已完成基因组测序的110个植物进行了鉴定，共发掘微卫星DNA位点26,230,099个，并为每个位点开发了3对引物。用户可获取目标物种有用的微卫星DNA位点和引物信息，以及每个位点所属物种、位置、起止、类型、大小以及序列信息。用户可以利用数据库进行微卫星DNA位点在线鉴定及分子标记在线设计。该数据库还提供了多种检索方式和下载功能，所有数据和分析结果都可下载。
该数据库为全球研究者们提供了在线的、友好的、便利的植物微卫星dna鉴定平台，同时还整合了在线微卫星DNA鉴定网络服务，是目前国际上涵盖最多植物物种和信息最全面的综合性数据库，填补了同领域相关研究空白。
原文链接：
PMDBase: a database for studying microsatellite DNA and marker development in plants
原文摘要：
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying microsatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMDBase, which integrates large amounts of microsatellite DNAs from genome sequenced plant species and includes a web service for microsatellite DNAs identification. In PMDBase, 26 230 099 microsatellite DNAs were identified spanning 110 plant species. Up to three pairs of primers were supplied for every microsatellite DNA. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and customized software. Furthermore, we developed MISAweb and embedded Primer3web to help users to identify microsatellite DNAs and design corresponding primers in their own genomic sequences online. All datasets of microsatellite DNAs can be downloaded conveniently. PMDBase will be updated regularly with new available genome data and can be accessed freely via the address http://www.sesame-bioinfo.org/PMDBase.
作者：张秀荣
