Genetic diversity analysis and fingerprint mapping construction of <i>Tilia amurensis</i> based on SSR molecular markers

Gao Lei; Liu Dan

doi:10.12171/j.1000-1522.20240399

Journal of Beijing Forestry University > 2025 > 47(3): 28-37. > DOI: 10.12171/j.1000-1522.20240399

Gao Lei, Liu Dan. Genetic diversity analysis and fingerprint mapping construction of Tilia amurensis based on SSR molecular markers[J]. Journal of Beijing Forestry University, 2025, 47(3): 28-37. DOI: 10.12171/j.1000-1522.20240399

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Genetic diversity analysis and fingerprint mapping construction of Tilia amurensis based on SSR molecular markers

Gao Lei^1,,
Liu Dan^2, ,

1.
College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, Shandong, China
2.
Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250100, Shandong, China

More Information

Received Date: November 25, 2024
Revised Date: December 16, 2024
Available Online: March 04, 2025

Graphical Abstract

Abstract

Abstract

Objective
Tilia amurensis is an important economic tree species and a nationally protected endangered tree species. Based on SSR molecular markers, this study analyzed the genetic diversity of Tilia amurensis from different provenances and constructed DNA fingerprinting profiles, aiming to provide references for the conservation of Tilia amurensis populations, the nationwide collection and preservation of germplasm resources, and the establishment of germplasm resource banks.
Method
A total of 173 Tilia amurensis samples from 16 provenances across 11 cities in 5 provinces in China were collected. SSR molecular markers were used for PCR amplification to analyze the genetic diversity of Tilia amurensis. Molecular variance analysis (AMOVA) and population clustering analysis were employed to investigate genetic differentiation among populations. Specific primers were selected to construct DNA fingerprinting profiles for Tilia amurensis.
Result
(1) From 12 primer pairs, 8 highly polymorphic and reproducible primer pairs were selected, collectively identifying 101 alleles, with an average of 12.6 alleles per polymorphic locus. The polymorphism information content (PIC) across loci ranged from 0.506 to 0.897, with a mean value of 0.739. (2) Only 4 primer pairs (C110, C840, D150, TC5) were required to effectively distinguish all Tilia amurensis individuals and construct their DNA fingerprinting profiles. (3) The genetic diversity of Tilia amurensis provenances was relatively high, with an effective number of alleles (N_e) of 4.937, Shannon’s information index (I) of 1.777, and Nei’s gene diversity (H) of 0.771. (4) Molecular variance analysis (AMOVA) revealed that 91% of genetic variation originated from within-population differences. (5) A phylogenetic tree constructed based on genetic distances classified the 16 provenances into 5 subclusters, with geographically proximate provenances clustering together, indicating closer genetic relationship.
Conclusion
The Tilia amurensis populations exhibit a relatively high overall level of genetic diversity, with moderate genetic differentiation observed. Intra-population genetic variation is predominant. Among the 16 populations, the seed sources from Wangqing, Jilin Province (JWQ3), Heilongjiang Province of northeastern China (HDN7, HDN8, HDN9), and Chengde City, Hebei Province of northern China (HCD15) show low genetic diversity levels and should be prioritized for in situ conservation and continuous monitoring. Populations JWQ2, JWQ4, JHL5, HNA10, LDD12, and LFX13 demonstrate higher genetic diversity and could serve as key targets for resource collection and conservation cultivation. This study provides a scientific basis for further research on population distribution, evolutionary patterns, and conservation strategies of Tilia amurensis in China.
- Tilia amurensis,
- SSR marker,
- genetic diversity,
- genetic differentiation,
- DNA fingerprint mapping,
- cluster analysis

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References (36)

References

[1]	王敏凤. 紫椴繁育技术研究进展[J]. 辽宁林业科技, 2023(5): 47−50. Wang M F. Research progress on Tilia amurensis breeding technology[J]. Liaoning Forestry Science and Technology, 2023(5): 47−50.
[2]	国家林业和草原局野生动植物保护司. 调整后的《国家重点保护野生植物名录》正式公布[EB/OL]. (2021)[2024−07−16]. https://www.forestry.gov.cn/c/www/lczc/10746.jhtml. Department of Wildlife Conservation. The revised list of wild plants under state key protection was officially released[EB/OL]. (2021)[2024−07−16]. https://www.forestry.gov.cn/c/www/lczc/10746.jhtml.
[3]	Lin S J, Wang Z M, Zhou H B, et al. A new micropropagation technology of Tilia amurensis : in vitro micropropagation of mature zygotic embryos and the establishment of a plant regeneration system[J]. Phyton-international Journal of Experimental Botany, 2024, 93(2): 277−289.
[4]	Chun S W, Lee J W, Ahn J Y. Development and characterization of novel microsatellite markers in Tilia amurensis Rupr. using next-generation sequencing[J]. Molecular Biology Reports, 2022, 49: 1−5. doi: 10.1007/s11033-021-06693-3
[5]	Zhang F G, Zhang S, Wu K, et al. Potential habitat areas and priority protected areas of Tilia amurensis Rupr. in China under the context of climate change[J]. Frontiers in Plant Science, 2024, 15: 1365264.
[6]	陈志祥, 罗小燕, 李拴林, 等. 基于SSR标记的木豆种质资源遗传多样性与群体结构分析[J]. 草地学报, 2021, 29(5): 904−911. Chen Z X, Luo X Y, Li S L, et al. Genetic diversity and population structure analysis of the pigeonpea (Cajanus cajan L.) germplasm resources based on SSR markers[J]. Acta Agrestia Sinica, 2021, 29(5): 904−911.
[7]	毛秀红, 郑勇奇, 孙百友, 等. 基于SSR的刺槐无性系遗传多样性分析和指纹图谱构建[J]. 林业科学, 2017, 53(10): 80−89. Mao X H, Zheng Y Q, Sun B Y, et al. Genetic diversity and fingerprints of Robinia pseudoacacia clones based on SSR markers[J]. Scientia Silvae Sinicae, 2017, 53(10): 80−89.
[8]	金玲, 刘明国, 董胜君, 等. 97个山杏无性系的遗传多样性及SSR指纹图谱[J]. 林业科学, 2018, 54(7): 51−61. Jin L, Liu M G, Dong S J, et al. Genetic diversity and fingerprints of 97 Prunus sibirica clones based on SSR markers[J]. Scientia Silvae Sinicae, 2018, 54(7): 51−61.
[9]	杨梦婷, 黄洲, 干建平, 等. SSR分子标记的研究进展[J]. 杭州师范大学学报(自然科学版), 2019, 18(4): 429−436. Yang M T, Huang Z, Gan J P, et al. Research progress of SSR molecular markers[J]. Journal of Hangzhou Normal University (Natural Science Edition), 2019, 18(4): 429−436.
[10]	叶冬梅, 吴晓萌, 段国珍, 等. 基于SSR分子标记分析白杄的群体遗传多样性[J/OL]. 分子植物育种, 2024. [2024−07−16]. http://kns.cnki.net/kcms/detail/46.1068.S.20230329.1043.008.html. Ye D M, Wu X M, Duan G Z, et al. The population genetic diversity of Picea meyeri based on SSR molecular markers[J/OL]. Molecular Plant Breeding, 2024. [2024−07−16]. http://kns.cnki.net/kcms/detail/46.1068.S.20230329.1043.008.html.
[11]	程玮哲, 樊军锋, 周永学, 等. 基于荧光SSR标记的10个白杨派种质资源遗传多样性分析[J]. 西北林学院学报, 2021, 36(3): 88−93. Cheng W Z, Fan J F, Zhou Y X, et al. Genetic diversity analysis of the 10 poplar accessions based on SSR molecular makers[J]. Journal of Northwest Forestry University, 2021, 36(3): 88−93.
[12]	吕晓娜, 范小青, 闫伯前, 等. 基于SSR标记的北京地方枣新品系的鉴定和亲缘关系分析[J/OL]. 分子植物育种, 2024. [2024−08−29]. http://kns.cnki.net/kcms/detail/46.1068.S.20231229.1055.004.html. Lü X N, Fan X Q, Yan B Q, et al. Identification and phylogenetic analysis of new jujube strains from Beijing region based on SSR markers[J/OL]. Molecular Plant Breeding; 2024. [2024−08−29]. http://kns.cnki.net/kcms/detail/46.1068.S.20231229.1055.004.html.
[13]	任重, 白倩, 苏淑钗. 基于SSR分子标记的中国黄连木遗传多样性分析[J]. 西北植物学报, 2022, 42(9): 1530−1539. Ren Z, Bai Q, Su S C. Genetic diversity analysis of Pistacia chinensis Bunge based on SSR markers[J]. Acta Botanica Boreali-occidentalia Sinica, 2022, 42(9): 1530−1539.
[14]	王欢利, 严灵君, 黄犀, 等. 南京椴群体遗传多样性和遗传结构分析[J]. 南京林业大学学报(自然科学版), 2023, 47(1): 145−153. Wang H L, Yan L J, Huang X, et al. Genetic diversity and genetic structure of Tilia miqueliana population[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 2023, 47(1): 145−153.
[15]	穆立蔷, 刘赢男. 不同地理分布区紫椴种群的遗传多样性变化[J]. 植物生态学报, 2007, 31(6): 1190−1198. Mu L Q, Liu Y N. Genetic diversity of Tillia amurensis populations in different geographical distribution regions[J]. Chinese Journal of Plant Ecology, 2007, 31(6): 1190−1198.
[16]	王东升. 山东省紫椴和野核桃AFLP遗传多样性研究[D]. 泰安: 山东农业大学, 2014. Wang D S. Genetic diversity study of Tillia amurensis Rupr. and Juglans cathayensis Dode from Shandong Province by AFLP markers [D]. Taian: Shandong Agricultural University, 2014.
[17]	林立, 林乐静, 祝志勇, 等. 93份槭树种质资源的SSR指纹图谱构建与遗传多样性分析[J]. 分子植物育种, 2022, 20(4): 1250−1263. Lin L, Lin L J, Zhu Z Y, et al. Construction of SSR fingerprint and genetic diversity analysis of 93 maple germplasm resources[J]. Molecular Plant Breeding, 2022, 20(4): 1250−1263.
[18]	Huang J, Ge X, Sun M. Modified CTAB protocol using a silica matrix for isolation of plant genomic DNA[J]. BioTechniques, 2000, 28(3): 432, 434.
[19]	岳远灏, 严灵君, 黄犀, 等. 基于全长转录组测序的南京椴EST-SSR标记开发[J/OL]. 分子植物育种, 2024. [2024−08−29]. http://kns.cnki.net/kcms/detail/46.1068.S.20220715.1525.008.html. Yue Y H, Yan L J, Huang X, et al. Development of EST-SSR markers based on transcriptome sequences of Tilia miqueliana maxim[J/OL]. Molecular Plant Breeding, 2024. [2024−08−29]. https://kns.cnki.net/kcms/detail/46.1068.S.20220715.1525.008.html.
[20]	Phuekvilai P, Wolff K. Characterization of microsatellite loci in Tilia platyphyllos (Malvaceae) and cross-amplification in related species[J]. Applications in Plant Sciences, 2013, 1(4): 1200386. doi: 10.3732/apps.1200386
[21]	燕丽萍, 吴德军, 毛秀红, 等. 基于SSR荧光标记的白蜡核心种质构建[J]. 中南林业科技大学学报, 2019, 39(7): 1−9. Yan L P, Wu D J, Mao X H, et al. Construction of core collection of Fraxinus based on SSR molecular markers[J]. Journal of Central South University of Forestry & Technology, 2019, 39(7): 1−9.
[22]	Peakall R O D, Smouse P E. GENALEX 6: genetic analysis in Excel: population genetic software for teaching and research[J]. Molecular Ecology Notes, 2006, 6(1): 288−295. doi: 10.1111/j.1471-8286.2005.01155.x
[23]	Krawczak M, Nikolaus S, Von E H, et al. PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships[J]. Community Genetics, 2006, 9(1): 55−61.
[24]	Balloux F, Lehmann L, de Meeûs T. The population genetics of clonal and partially clonal diploids[J]. Genetics, 2003, 164(4): 1635−1644. doi: 10.1093/genetics/164.4.1635
[25]	侯立娜, 李慧, 王天琪, 等. 金银花及近缘种遗传多样性分析及SSR指纹图谱构建[J]. 分子植物育种, 2024, 22(19): 6382−6389. Hou L N, Li H, Wang T Q, et al. Genetic diversity analysis and SSR fingerprint construction of Lonicera japonica and its related species[J]. Molecular Plant Breeding, 2024, 22(19): 6382−6389.
[26]	Wu Q C, Zhang Y, Xie X M, et al. Analysis of the genetic diversity and population structure of Tilia amurensis from China using SSR markers: implications for conservation[J]. Global Ecology and Conservation, 2024, e03173.
[27]	Wright S. Evolution and the genetics of populations: experimental results and evolutionary deductions[M]. Vol. 3. Chicago: University of Chicago Press, 1984;515−520.
[28]	Wright S. Evolution in Mendelian populations[J]. Genetics, 1931, 16(2): 97−159. doi: 10.1093/genetics/16.2.97
[29]	Chen B R, Zou H, Zhang X Y, et al. Distribution change and protected area planning of Tilia amurensis in China: a study of integrating the climate change and present habitat landscape pattern[J]. Global Ecology and Conservation, 2023(43): e02438.
[30]	Lobo A, Hansen O K, Hansen J K, et al. Local adaptation through genetic differentiation in highly fragmented Tilia cordata populations[J]. Ecology and Evolution, 2018, 8(12): 5968−5976. doi: 10.1002/ece3.4131
[31]	简曙光, 唐恬, 张志红, 等. 中国银叶树种群及其受威胁原因[J]. 中山大学学报(自然科学版), 2004, 43(增刊1): 91−96. Jian S G, Tang T, Zhang Z H, et al. The population characteristics and endangered causes of Heritiera littoralis dryand in China[J]. Acta Scientiarum Naturalium Universitatis Sunyatseni, 2004, 43(Suppl. 1): 91−96.
[32]	Hamrick J L, Godt M J W, Sherman-Broyles S L. Factors influencing levels of genetic diversity in woody plant species[J]. Forestry Sciences, 1992(6): 95−124.
[33]	田忠琼. 濒危植物水青树SSR分子标记的开发与群体遗传结构的研究[D]. 南充: 西华师范大学, 2020. Tian Z Q. The development of SSR markers and geneticstructure analysis of an endangered plant Tetracentron sinense Oliv. [D]. Nanchong: China West Normal University, 2020.
[34]	李思琪, 张文臣, 杨柳, 等. 基于SSR标记的文冠果遗传多样性分析及指纹图谱构建[J]. 生物技术通报, 2024, 40(5): 74−83. Li S Q, Zhang W C, Yang L, et al. Genetic diversity analysis and DNA fingerprint construction based on SSR markers for Xanthoceras sorbifolia[J]. Biotechnology Bulletin, 2024, 40(5): 74−83.
[35]	刘加能, 潘登浪, 程秋如, 等. 基于SSR标记的油棕核心种质筛选及DNA指纹图谱构建[J/OL]. 分子植物育种, 2024, [2025−02−28]. http://kns.cnki.net/kcms/detail/46.1068.s.20240318.1734.016.html. Liu J N, Pan D L, Cheng Q R, et al. Selection of oil palm core germplasm and DNA fingerprinting construction based on SSR markers [J/OL]. Molecular Plant Breeding, 2024, [2025−02−28]. http://kns.cnki.net/kcms/detail/46.1068.s.20240318.1734.016.html.
[36]	李慧, 侯立娜, 王天琪, 等. 基于SSR标记的皱皮木瓜遗传多样性分析及品种分子身份证构建[J]. 南京林业大学学报(自然科学版), 2025, 49(1): 59−70. Li H, Hou L N, Wang T Q, et al. The genetic diversity analysis and molecular ID establishment of Chaenomeles speciosa based on SSR markers[J]. Journal of Nanjing Forestry University (Natural Sciences Edition), 2025, 49(1): 59−70.

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Genetic diversity analysis and fingerprint mapping construction of Tilia amurensis based on SSR molecular markers