Hou Qiqi, Ji Weihong, An Kang, Tan Yuchen, Liu Penghui, Su Junhu
Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural College, Gansu Agricultural University, Lanzhou, 730070, China.
Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China.
Sci Rep. 2025 Jan 2;15(1):524. doi: 10.1038/s41598-024-84631-6.
Microsatellite markers are cost-effective, rapid, efficient, and show great advantages in in large-sample kinship analysis and population structure studies. However, microsatellite loci are seriously underdeveloped in non-model organisms. The plateau zokor (Eospalax baileyi) is a key species living underground in the Tibetan Plateau, the effective management of which has long been challenging. In this study, we analyzed the distribution characteristics and functions of microsatellites in the genome of plateau zokors, and their polymorphic sites. The mononucleotide and dinucleotide types being the most abundant in the genome. The largest number of microsatellites and their abundance in the intergenic region whereas the smallest number of microsatellites and their abundance in the coding region. The coding sequences containing microsatellites were annotated to 52 major functional genes and assigned 19,358 Gene Ontology entries. The Kyoto Encyclopedia of Genes and Genomes pathway was the most enriched in the signal transduction pathway. Thirteen pairs of polymorphic loci were successfully amplified, with the number of alleles ranging from 3 to 8, observed heterozygosity ranging from 0.059 to 0.810, and expected heterozygosity ranging from 0.469 to 0.854. These microsatellite markers provide a cornerstone for studies on the identification of parentage and population genetics of plateau zokors.
微卫星标记具有成本效益高、快速、高效的特点，并且在大样本亲缘关系分析和群体结构研究中显示出巨大优势。然而，微卫星位点在非模式生物中严重发育不足。高原鼢鼠（Eospalax baileyi）是青藏高原地下生活的关键物种，对其进行有效管理长期以来一直具有挑战性。在本研究中，我们分析了高原鼢鼠基因组中微卫星的分布特征和功能及其多态性位点。单核苷酸和二核苷酸类型在基因组中最为丰富。微卫星数量及其丰度在基因间区域最多，而在编码区域最少。含有微卫星的编码序列被注释到52个主要功能基因，并被赋予19358个基因本体条目。京都基因与基因组百科全书通路在信号转导通路中富集程度最高。成功扩增出13对多态性位点，等位基因数范围为3至8，观察杂合度范围为0.059至0.810，预期杂合度范围为0.469至0.854。这些微卫星标记为高原鼢鼠的亲权鉴定和群体遗传学研究提供了基石。
