Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud)

Ramie (Boehmeria nivea L. Gaud) is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strategies have been hampered by the shortage of simple sequence repeat (SSR) markers. In our previous study, we had assembled de novo 43,990 expressed sequence tags (ESTs). In the present study, we searched these previously assembled ESTs for SSRs and identified 1,685 ESTs (3.83%) containing 1,878 SSRs. Next, we designed 1,827 primer pairs complementary to regions flanking these SSRs, and these regions were designated as SSR markers. Among these markers, dinucleotide and trinucleotide repeat motifs were the most abundant types (36.4% and 36.3%, respectively), whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented苎麻（Boehmeria nivea L. Gaud）是最重要的天然纤维作物之一，提升纤维产量与品质是其优良品种选育工作的核心目标。然而，由于简单序列重复（simple sequence repeat, SSR）标记资源匮乏，解析苎麻遗传机制、开发高效育种策略的相关研究长期受阻。本课题组前期研究中完成了43990条表达序列标签（expressed sequence tags, ESTs）的从头组装。本研究针对上述已组装的ESTs开展SSR位点检索，最终鉴定出1685条包含1878个SSR位点的ESTs，占比为3.83%。随后，我们针对这些SSR位点的侧翼序列设计了1827对引物，并将其划定为SSR标记。在该批标记中，二核苷酸与三核苷酸重复基元为最丰富的类型，占比分别为36.4%与36.3%，而四核苷酸、五核苷酸及六核苷酸重复基元占比