中南林业科技大学学报

香椿全基因组SSR位点分析及分子标记开发

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郑名敏 ¹ , 刘孝伟 ² , 虞秋雨 ¹ , 李杨 ¹ , 曾睿 ¹ , 高云洪 ³ , 杨敏 ⁴

中南林业科技大学学报 | 生物学 2026,46(5): 149-157

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中南林业科技大学学报 |生物学 2026 , 46 (5) : 149 -157

香椿全基因组SSR位点分析及分子标记开发

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郑名敏¹, 刘孝伟², 虞秋雨¹, 李杨¹, 曾睿¹, 高云洪³, 杨敏⁴

作者信息

^1.成都师范学院　a. 特色园艺生物资源开发与利用四川省高校重点实验室；b. 化学与生命科学学院，四川　成都　611130

^2.成都农业科技职业学院　农学园艺学院，四川　成都　611130

^3.四川益仲农业开发有限公司，四川　成都　610213

^4.四川省内江市农业科学院，四川　内江　641000

作者简介:

郑名敏（4648442@qq.com），讲师，博士。

Genome-wide analysis of simple sequence repeats and development of molecular markers in Toona sinensis

Mingmin ZHENG¹, Xiaowei LIU², Qiuyu YU¹, Yang LI¹, Rui ZENG¹, Yunhong GAO³, Min YANG⁴

Affiliations

^1.a. Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources; b. College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, Sichuan, China

^2.School of Agriculture and Horticulture, Chengdu Agricultural College, Chengdu 611130, Sichuan, China

^3.Sichuan Yizhong Agricultural Development Company, Chengdu 610213, Sichuan, China

^4.Neijiang Academy of Agricultural Sciences, Neijiang 641000, Sichuan, China

出版时间: 2026-05-25 doi: 10.14067/j.cnki.1673-923x.2026.05.015

文章导航

摘要

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【目的】

系统分析香椿基因组中SSR序列的分布模式及特征，批量开发高效的分子标记，为香椿种质资源鉴定、遗传多样性分析、遗传图谱构建及分子标记辅助育种等提供理论依据和技术支持。

【方法】

基于已公布的香椿品种‘黑油椿’参考基因组序列，利用MISA软件对基因组中1～6核苷酸重复的SSR位点进行搜索，分析其分布模式及特征，结合Primer 3.0软件和电子PCR进行批量SSR引物设计。随机选取20对SSR引物在6份香椿材料中进行PCR扩增，通过聚丙烯酰胺凝胶电泳检验引物的有效性和多态性。

【结果】

在全基因组28条染色体上共鉴定到308 421个SSR位点，平均每1.92 kb出现1个SSR位点，各染色体间SSR分布频率差异较小。其中，单核苷酸和二核苷酸为主要重复类型，分别占SSR总数的59.23%和31.08%。共检测到979种不同的SSR基元类型，其中A/T、AT/TA和AAT/ATT为优势基元，基因组SSR序列中A、T碱基占绝对优势。香椿基因组SSR序列长度为10～1 218 bp，各核苷酸重复类型长度越长，SSR位点数量越少。根据SSR位点侧翼的保守序列成功设计104 813对SSR引物，随机合成20对SSR引物，有18对能扩增出符合预期的条带，有效扩增率为90.0%；其中9对引物的扩增产物表现出多态性，多态性比例为50.0%。

【结论】

本研究揭示了香椿基因组中SSR的分布特征，并批量开发了一系列SSR引物，为后续香椿遗传育种及相关研究提供了丰富的分子标记资源。

关键词

香椿 / 基因组 / SSR / 标记开发

Abstract

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【Objective】

A systematic analysis of SSR loci in the genome and the development of efficient molecular markers was accomplished to provide a theoretical basis and technical support for further research on germplasm identification, genetic diversity analysis, linkage map construction, and molecular marker-assisted breeding in T. sinensis.

【Method】

Based on the published reference genome of the cultivar ‘Heiyouchun’, genome-wide SSR loci containing 1-6 nucleotide repeats were identified using the MISA software, and the distribution patterns and characteristics of SSR types were comprehensively analyzed. SSR primers were developed using Primer3.0 in combination with in silico PCR. Subsequently, 20 pairs of SSR primers were randomly selected for PCR amplification using genomic DNA from six T. sinensis samples. The validity and polymorphism of these primers were evaluated using polyacrylamide gel electrophoresis (PAGE).

【Result】

A total of 308 421 SSR loci were identified in the genome of T. sinensis, with an average of one locus per 1.92 kb. The distribution frequency of SSRs was relatively uniform across the chromosomes. Mononucleotide and dinucleotide repeats were the predominant types, accounting for 59.23% and 31.08% of the total SSRs, respectively. Across the entire genome, 979 distinct SSR motif types were identified. Among these, A/T, AT/TA, and AAT/ATT motifs occurred most frequently, indicating that A and T bases were predominant in the SSR sequences of the T. sinensis genome. The length of SSR sequences in the T. sinensis genome ranged from 10 to 1 218 bp, and the number of SSR loci decreased with increasing repeat length across all nucleotide repeat motifs. A total of 104 813 pairs of SSR primers were designed based on the flanking sequences of the SSR loci. Among the 20 pairs of primers synthesized, 18 pairs of primers amplified the target bands with an amplification efficiency of 90.0%. Additionally, products from nine primer pairs exhibited polymorphism, and the polymorphism rate reached 50.0%.

【Conclusion】

This study elucidated the distribution characteristics of SSRs in the T. sinensis genome and developed a large set of genome-wide SSR markers, providing valuable molecular tools for future genetic studies and breeding applications in T. sinensis.

Key words

Toona sinensis / genome / SSR / marker development

引用本文

郑名敏, 刘孝伟, 虞秋雨, 李杨, 曾睿, 高云洪, 杨敏. 香椿全基因组SSR位点分析及分子标记开发. 中南林业科技大学学报, 2026 , 46 (5) : 149 -157 . DOI: 10.14067/j.cnki.1673-923x.2026.05.015

Mingmin ZHENG, Xiaowei LIU, Qiuyu YU, Yang LI, Rui ZENG, Yunhong GAO, Min YANG. Genome-wide analysis of simple sequence repeats and development of molecular markers in Toona sinensis[J]. Journal of Central South University of Forestry & Technology, 2026 , 46 (5) : 149 -157 . DOI: 10.14067/j.cnki.1673-923x.2026.05.015

基金

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中央引导地方科技发展专项(2024ZYD0040)
成都师范学院高层次人才引进项目(YJRC2020-23)
大学生创新创业训练计划项目(S202214389166)

参考文献

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2026年第46卷第5期

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文章信息

doi: 10.14067/j.cnki.1673-923x.2026.05.015

接收时间：2025-05-30
首发时间：2026-10-30
出版时间：2026-05-25

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出版历史

收稿日期：2025-05-30
修回日期：2025-07-25

基金

中央引导地方科技发展专项(2024ZYD0040)

成都师范学院高层次人才引进项目(YJRC2020-23)

大学生创新创业训练计划项目(S202214389166)

作者信息

^1.成都师范学院　a. 特色园艺生物资源开发与利用四川省高校重点实验室；b. 化学与生命科学学院，四川　成都　611130

^2.成都农业科技职业学院　农学园艺学院，四川　成都　611130

^3.四川益仲农业开发有限公司，四川　成都　610213

^4.四川省内江市农业科学院，四川　内江　641000

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2种不同金属材料的力学参数

科 Family	属数 Number of genus	种数 Number of species	占总种数比例 Percentage of total species (%)	属 Genus	种数 Number of species	占总种数比例 Percentage of total species (%)
鹅膏菌科Amanitaceae	2	11	5.26	鹅膏菌属 Amanita	10	4.78
小菇科 Mycenaceae	2	12	5.74	丝盖伞属 Inocybe	5	2.39
多孔菌科 Polyporaceae	8	14	6.70	蜡蘑属 Laccaria	5	2.39
红菇科 Russulaceae	3	23	11.00	小皮伞属 Marasmius	6	2.87
				小菇属 Mycena	11	5.26
				光柄菇属 Pluteus	5	2.39
				红菇属 Russula	17	8.13
				栓菌属 Trametes	5	2.39

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