State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
J Appl Genet. 2020 Sep;61(3):367-377. doi: 10.1007/s13353-020-00561-9. Epub 2020 Jun 7.
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.
简单序列重复（SSR）标记因其高度的重现性、多态性和丰富性，常用于许多遗传应用，如图谱构建、指纹图谱和遗传多样性分析。内源性 miRNAs 在植物发育和基因表达中起着至关重要的作用，可应对各种生物和非生物胁迫条件。在本研究中，我们从 287 个前体 miRNAs 中预测了 110 个 miRNA-SSR 引物对。在 110 对引物中，有 85 对成功扩增，并检验了它们在其他禾本科和非禾本科物种中的可转移性。结果表明，所有 82 对引物都产生了明确而强烈的扩增，在 23 个研究的 Cleistogenes 个体中，共产生了 385 个多态性等位基因。每个引物产生的等位基因数量从 3 到 11 不等，平均每个位点为 4.69。预期杂合度（He）范围为 0.44 到 0.88，平均每个位点为 0.74，多态信息含量（PIC）值范围为 0.34 到 0.87，平均每个位点为 0.69。此外，利用 GO（基因本体论）和 KEGG（京都基因与基因组百科全书）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。
