College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
Genome. 2011 Sep;54(9):763-70. doi: 10.1139/g11-042. Epub 2011 Sep 7.
Numerous quantitative trait loci (QTL) have been detected in Brassica species, but fine-mapping of major QTL has advanced slowly. The development of functional markers can overcome this barrier. We used publicly available PlantGDB-assembled unique transcripts (PUTs) from Brassica species to design 7836 functional simple sequence repeat (SSR) primer pairs. Functional annotation of the PUTs containing SSRs was done by Blast2GO. The PUTs harbouring SSRs were mainly involved with nucleotide or protein binding and enzyme activity, and preferentially functioned in membranes and cytoplasm. Totally, 210 PUT primer pairs were selected to test their polymorphism, stability, and PCR quality. Approximately 70% (147) of the primer pairs resulted in successful amplification with an average polymorphic information content (PIC) value of 0.49. The highest level of polymorphism was dinucleotide repeat SSRs, followed by tri- and mononucleotide repeats. Approximately 60% of the primer pairs showed good transferability among Brassica species. These results show that the development of markers from PUTs is a feasible and simple approach to develop functional SSR markers on a large scale across Brassica species. In addition, these markers can provide a novel alternative that is a putative approach for rapid determination of candidate genes, genetic mapping, genetic diversity analysis, and comparative mapping in Brassica species.
已经在芸薹属物种中检测到许多数量性状位点（QTL），但主要 QTL 的精细定位进展缓慢。功能标记的开发可以克服这一障碍。我们使用来自芸薹属物种的公开可用的 PlantGDB 组装的独特转录本（PUT）设计了 7836 对功能性简单重复序列（SSR）引物。通过 Blast2GO 对包含 SSR 的 PUT 进行了功能注释。含有 SSR 的 PUT 主要参与核苷酸或蛋白质结合和酶活性，并且优先在膜和细胞质中发挥作用。总共选择了 210 对 PUT 引物来测试它们的多态性、稳定性和 PCR 质量。大约 70%（147 个）的引物对成功扩增，平均多态信息含量（PIC）值为 0.49。二核苷酸重复 SSR 的多态性最高，其次是三核苷酸和单核苷酸重复。大约 60%的引物对在芸薹属物种之间具有良好的可转移性。这些结果表明，从 PUT 开发标记是一种可行且简单的方法，可以在芸薹属物种中大规模开发功能 SSR 标记。此外，这些标记可以提供一种新的替代方法，用于快速确定候选基因、遗传作图、遗传多样性分析和芸薹属物种的比较作图。
