| 基于麦冬转录组数据的SSR序列特征分析及引物设计 |
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| 引用本文：王 钧，戴 维，赖强龙，叶坤浩，陈 杰，冯 伦，刘 媛，何爱坪，赵 丹.基于麦冬转录组数据的SSR序列特征分析及引物设计[J].西北农业学报,2025,(2):300~308 |
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| 基金项目:四川省科技计划项目（2021YFYZ0012，2021ZHFP0118）；中央本级重大增减支项目：名贵中药资源可持续利用能力建设项目（2060302）；财政部和农业农村部：国家现代农业产业技术体系（CARS-21）；绵阳市农业科学研究院创新基金（Cxjj89）。 |
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| 中文摘要:采用高通量测序技术获得了麦冬转录组53 466条Unigenes，并通过序列分析识别出35 832个SSR位点，分布于24 539条Unigenes上，SSR出现频率高达67.02%，平均分布距离为4.88 kb。对包含SSR位点的24 539条Unigenes进行GO和KEGG注释，结果显示主要集中于生物学过程、植物-病原体互作等基因功能和代谢通路。从SSR重复基元类型来看，单核苷酸重复数目最多，占比57.06%，其中A/T为绝对优势类型，有20 193个；五核苷酸重复平均分布距离最高，为4 069.34 kb。从重复次数来看，基元重复10次以上的类型数目最多，有20 849个，占比61.69%。随机挑选30个不同类型的SSR基元位点并设计引物，对川麦冬、浙麦冬基因组DNA进行PCR扩增，结果显示28对引物可以在两个栽培种中扩增出条带，其中16对引物可扩增出目的条带。 |
| 中文关键词:麦冬 转录组 SSR位点 引物设计 |
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| Analysis of SSR Sequence Characteristics and Primers Design Based on Transcriptome Data of Ophiopogon japonicus |
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| Abstract:Ophiopogon japonicus, a medicinal plant in the Liliaceae family, is listed as the supreme herb for nourishing Yin and moistening the lung in the Shennong’s Classic of Materia Medica. This study employed high-throughput sequencing technology to obtain a total of 53 466 Unigenes from the transcriptome of O.japonicus. A total of 35 832 SSR loci were identified in the Unigenes through sequence analysis. They were distributed across 24 539 Unigenes, with a high SSR occurrence frequency of 67.02% and an average distribution distance of 4.88 kb. GO and KEGG annotations of 24 539 Unigenes containing SSR loci revealed their main involvement in biological processes, plant-pathogen interaction, and other gene functions and metabolic pathways. Mononucleotide repeats were the most abundant, accounting for 57.06%, with A/T (20 193) being the absolute dominant type among all SSR repeat units. Pentonucleotide repeats had the highest average distribution distance (4 069.34 kb). From the perspective of repeat times, the types with repeat unit 10 or more had the most, with 20 849 ones, accounting for 61.69%. 30 different repeats types were randomly selected and primers were designed to amplify the genomic DNA of Chuan-maidong (O.japonicus from Sichuan) and Zhe-maidong (O.japonicus from Zhejiang). The results showed that 28 pairs of primers could amplify bands in two cultivars, of which 16 pairs could amplify the target band. This study explored rich SSR loci information from the transcriptome data of O.japonicus, providing data and research foundation for genetic evaluation of resources and molecular marker assisted breeding research. |
| keywords:Ophiopogon japonicus Transcriptome SSR loci Primer design |
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