Key Laboratory of Ministry of Education for Plant Development Biology, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.
J Hered. 2010 Jan-Feb;101(1):71-82. doi: 10.1093/jhered/esp070.
Expressed sequence tags (ESTs) provide a valuable resource for the development of simple sequence repeat (SSR) or microsatellite markers. This study identified SSRs within ESTs from Nelumbo nucifera (lotus or sacred lotus), developed markers from them, and assessed the potential of those markers for diversity analysis. Within 2207 ESTs from N. nucifera downloaded from GenBank, 1483 unigenes (303 contigs and 1180 singletons) were identified. After eliminating for redundancy, 125 SSR-containing ESTs were derived, and 71 unique SSRs were detected with an average density of one SSR per 13.04 kb. Dinucleotide repeats were the dominant motif in N. nucifera, whereas the sequences AG/TC/GA/CT, AAG/TTC/GAT/AGA, and AAAGCC were the most frequent of di-, tri-, and hexanucleotide motifs, respectively. The AG/TC (40.85%) and AAG (5.63%) motifs were predominant for the di- and trinucleotide repeats, respectively. Sixty-two SSR-containing ESTs were suitable for primer design. From these sequences, 23 EST-SSR markers were developed and were applied to 39 cultivated varieties of N. nucifera, 10 accessions of wild N. nucifera, and 1 accession of Nelumbo lutea (American lotus). Genetic diversity and genetic relationships were examined by constructing unweighted pair-group method with arithmetic average dendrograms and principal coordinates analysis plots based on SSR polymorphisms. Results indicated genetic differentiation between cultivated and wild lotus and between seed lotus cultivars and rhizome lotus cultivars. These EST-SSR markers will be useful for further studies of the evolution and diversity of Nelumbo.
表达序列标签 (EST) 为简单序列重复 (SSR) 或微卫星标记的开发提供了有价值的资源。本研究从Nelumbo nucifera（莲花或圣莲）的 EST 中鉴定 SSR，从它们中开发标记，并评估这些标记用于多样性分析的潜力。在从 GenBank 下载的 2207 个 N. nucifera EST 中，鉴定出 1483 个基因（303 个重叠群和 1180 个单基因）。消除冗余后，从 EST 中衍生出 125 个含有 SSR 的 EST，检测到 71 个独特的 SSR，平均每 13.04kb 有一个 SSR。二核苷酸重复是 N. nucifera 的主要基序，而 AG/TC/GA/CT、AAG/TTC/GAT/AGA 和 AAAGCC 分别是二核苷酸、三核苷酸和六核苷酸基序中最常见的序列。AG/TC（40.85%）和 AAG（5.63%）基序分别是二核苷酸和三核苷酸重复的主要基序。62 个含有 SSR 的 EST 适合引物设计。从这些序列中，开发了 23 个 EST-SSR 标记，并将其应用于 39 个栽培品种的 N. nucifera、10 个野生 N. nucifera 品系和 1 个 Nelumbo lutea（美国莲花）品系。通过构建基于 SSR 多态性的无加权对群方法算术平均聚类图和主坐标分析图，研究了遗传多样性和遗传关系。结果表明，栽培莲与野生莲、子莲品种与藕莲品种之间存在遗传分化。这些 EST-SSR 标记将有助于进一步研究 Nelumbo 的进化和多样性。
