Simple sequence repeat (SSR) markers are commonly used for many genetic applications, such as map construction, fingerprinting, and genetic diversity analyses, due to their high reproducibility, polymorphism, and abundance. Endogenous miRNAs play essential roles in plant development and gene expression under diverse biotic and abiotic stress conditions. In the present study, we predicted 110 miRNA-SSR primer pairs from 287 precursor miRNAs. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other Gramineae and non-Gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. Furthermore, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. In conclusion, the results showed that an miRNA-based microsatellite marker system can be applicable for genetic diversity and marker-assisted breeding studies.

中文翻译：

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在 Cleistogenes songorica 中基于 miRNA 的 SSR 标记的全基因组开发及其对禾本科/非禾本科物种的转移性分析。

简单序列重复 (SSR) 标记因其高重现性、多态性和丰度而常用于许多遗传应用，例如图谱构建、指纹识别和遗传多样性分析。内源性 miRNA 在不同生物和非生物胁迫条件下的植物发育和基因表达中发挥重要作用。在本研究中，我们从 287 个前体 miRNA 中预测了 110 个 miRNA-SSR 引物对。在 110 对引物中，有 85 对被成功扩增并检查了对其他禾本科和非禾本科物种的可转移性。结果表明，所有 82 个引物对都产生了明确且强的扩增，并且在 23 个研究的Cleistogenes 中种质中，共有 385 个等位基因是多态的。每个引物产生的等位基因数从 3 到 11 不等，每个基因座平均为 4.69。预期杂合度 (He) 范围为 0.44 至 0.88，每个基因座的平均值为 0.74，PIC（多态性信息含量）值范围为 0.34 至 0.87，每个基因座的平均值为 0.69。此外，使用GO（基因本体论）和KEGG（京都基因和基因组百科全书）数据库预测和分析了1422个miRNA靶基因。总之，结果表明基于 miRNA 的微卫星标记系统可适用于遗传多样性和标记辅助育种研究。