Genetic diversity analysis and simple sequence repeat fingerprint construction of Acer truncatum bunge germplasm from udantara natural reserve, China
DOI:
https://doi.org/10.14393/BJ-v41n0a2025-74742Keywords:
Acer truncatum Bunge, Fingerprint, Genetic diversity, Population structure, SSR maker.Abstract
Acer truncatum Bunge is an ecologically and economically indigenous tree species in China, which is valued for ornamental, medicinal, and ecological contributions. As a major natural population of A. truncatum in China, the Udantara Natural Reserve harbors critical genetic resources for this species. To enhance genetic understanding and support conservation efforts, we analyzed the genetic diversity and population structure of 104 A. truncatum germplasm from Udantara using 20 pairs of simple sequence repeat (SSR) primers. Totally, 137 alleles were amplified, including 58.060 effective alleles. The average number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and Shannon’s information index (I) were 6.850, 2.903, 0.424, 0.591, and 1.182, respectively, and the polymorphism information content (PIC) of the markers ranged between 0.293–0.839, with an average of 0.548, indicating moderate-to-high informativeness. The structure analysis partitioned the germplasm into two distinct genetic groups (28 and 76 individuals, respectively). Additionally, five SSR primers were identified as sufficient for generating unique genetic fingerprints for all 104 germplasm. Based on these findings, we propose a dual conservation strategy that integrates in situ protection of natural habitats within Udantara and ex situ preservation through a nationwide germplasm repository. Further recommendations include expanding the genetic representation by collecting germplasm across China and developing novel variants via hybridization and selective introduction. This study provides foundational genetic insights and actionable strategies to safeguard the biodiversity of A. truncatum, ensuring its ecological resilience and sustainable utilization in China.
References
AKASH, M., et al. Development and validation of gene-based SSR markers in the genus Mesembryanthemum. Scientifica. 2023, 2023, 6624354. https://doi.org/10.1155/2023/6624354
AMITEYE, S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon. 2021, 7, e08093. https://doi.org/10.1016/j.heliyon.2021.e08093
BABAY, E., et al. Quality selection and genetic diversity of Tunisian durum wheat varieties using SSR markers. Bioscience Journal. 2019, 35, 1002–1012. https://doi.org/10.14393/BJ-v35n4a2019-42301
BADRI, M. and LUDIDI, N. Germplasm conservation for biotechnology and plant breeding. In: KAMALUDDIN, KIRAN, U. and ABDIN M. Z., eds. Technologies in plant biotechnology and breeding of field crops. Singapore: Springer Nature Singapore, 2022.
BAO, H. S. G. W., et al. Present situation, existing problems and countermeasures of protection, development and utilization of Acer truncatum germplasm resources in Tongliao area. Forestry Science & Technology. 2019, 44, 53–56. https://doi.org/10.19750/j.cnki.1001-9499.2019.06.016
BORGES DO VAL, A. D., et al. Use of molecular markers SSR and SCAR for identification of olive accessions. Bioscience Journal. 2020, 36, 1137–1145. https://doi.org/10.14393/BJ-v36n4a2020-47959
CHEN, G., et al. Analysis of genetic diversity and fingerprint construction of Acer resources in Liaoning Province by SRAP. Journal of Shenyang Agricultural University. 2016, 47, 425–431. https://doi.org/10.3969/j.issn.1000-1700.2016.04.007
CHENG, D. K., et al. Acer truncatum Bunge seed oil ameliorated oxaliplatin-induced demyelination by improving mitochondrial dysfunction via the Pink1/Parkin mitophagy pathway. Food & Function. 2024, 15, 1355−1368. https://doi.org/10.1039/d3fo03955b
CISTERNAS-FUENTES, A., et al. Evolution of selfing syndrome and its influence on genetic diversity and inbreeding: A range-wide study in Oenothera primiveris. American Journal of Botany. 2022, 109, 789−805. https://doi.org/10.1002/ajb2.1861
ENGELS, J. M. M. and EBERT, A. W. A critical review of the current global ex situ conservation system for plant agrobiodiversity. II. strengths and weaknesses of the current system and recommendations for its improvement. Plants (Basel). 2021, 10, 1904. https://doi.org/10.3390/plants10091904
EVANNO, G., REGNAUT, S., and GOUDET, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology. 2005, 14, 2611−2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
GADE, P., et al. Assessment of wheat variety adoption in Bangladesh through DNA fingerprinting. Crop Science. 2021, 61, 3564−3577. https://doi.org/10.1002/csc2.20579
HAN, Z. Q., et al. Construction of polymorphic SSR primer library and germplasm resource fingerprint database of Populus tomentosa. Journal of Beijing Forestry University. 2019, 41, 10−18. https://doi.org/10.13332/j.1000-1522.20190040
HEYWOOD, V. H. Conserving plants within and beyond protected areas – still problematic and future uncertain. Plant Diversity. 2019, 41, 36-49. https://doi.org/10.1016/j.pld.2018.10.001
HUSSEIN, M. A. A., et al. Comparative assessment of SSR and RAPD markers for genetic diversity in some mango cultivars. PeerJ. 2023, 11, e15722. https://doi.org/10.7717/peerj.15722
KARIHALOO, J. L. DNA fingerprinting techniques for plant identification. In: BAHADUR, B., VENKAT RAJAM, M., SAHIJRAM, L., and KRISHNAMURTHY K., eds. Plant biology and biotechnology. New Delhi: Springer India, 2015.
LE, X. N., et al. Research on the differences in phenotypic traits and nutritional composition of Acer truncatum Bunge seeds from various regions. Foods (Basel, Switzerland). 2023, 12, 2444. https://doi.org/10.3390/foods12132444
LI, D., et al. Development and application of EST-SSR markers for DNA fingerprinting and genetic diversity analysis of the main cultivars of black locust (Robinia pseudoacacia L.) in China. Forests. 2019a, 10(8), 644. https://doi.org/10.3390/f10080644
LI, J. B., et al. Transcriptional regulation of the Acer truncatum B. response to drought and the contribution of AtruNAC36 to drought tolerance. Antioxidants (Basel, Switzerland). 2023, 12, 1339. https://doi.org/10.3390/antiox12071339
LI, Q., et al. A mini review of nervonic acid: Source, production, and biological functions. Food Chemistry. 2019b, 301, 125286. https://doi.org/10.1016/j.foodchem.2019.125286
LI, Q. M., et al. Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly. Plant Diversity. 2022, 44, 271−278. https://doi.org/10.1016/j.pld.2021.11.002
LIAO, J., et al. Spatial pattern of genetic diversity and demographic history revealed by population genomic analysis: resilience to climate fluctuations of Acer truncatum Bunge. Forests, 15, 639. https://doi.org/10.3390/f15040639
LIN, L., et al. Construction of SSR fingerprint and genetic diversity analysis of 93 maple germplasm resources. Molecular Plant Breeding. 2022, 20, 1250–1263. https://doi.org/10.13271/j.mpb.020.001250
LIU, L. T., et al. Seed germination characteristics of a critically endangered evergreen oak - Quercus marlipoensis (Fagaceae) and their conservation implications. Forests. 2024, 15, 235. https://doi.org/10.3390/f15020235
LONG, Y., et al. Development of novel genomewide simple sequence repeat markers for Acer truncatum Bunge and assessment of their transferability to other closely related species. Forests, 2024, 15, 635. https://doi.org/10.3390/f15040635
LUO, Q., et al. Analysis on genetic diversity of first filial generation and second filial generation of Acer yangjuechi based on SSR markers. Journal of Plant Resources and Environment, 2022, 31, 66–73. https://doi.org/10.3969/j.issn.1674-7895.2022.05.08
MORCIA, C., et al. Long-term in situ conservation drove microevolution of solina d’abruzzo wheat on adaptive, agronomic and qualitative traits. Plants. 2023, 12, 1306. https://doi.org/10.3390/plants12061306
MOTAHARI, B., et al. Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers. Gene. 2021, 769, 145245. https://doi.org/10.1016/j.gene.2020.145245
QIAO, Q., et al. Analysis of leaf morphology variation and genetic diversity via SRAP markers for near-threatened plant Acer truncatum. Global Ecology and Conservation, 2022, 33, e01980. https://doi.org/10.1016/j.gecco.2021.e01980
QIAO, Q., et al. Oil content and nervonic acid content of Acer truncatum seeds from 14 regions in China. Horticultural Plant Journal. 2019, 5, 24−30. https://doi.org/10.1016/j.hpj.2018.11.001
REZK, A. A., MOHAMED, H. I., and EL-BELTAGI, H. S. Genetic variability and diversity analysis in Oryza sativa L. genotypes using quantitative traits and SSR markers. Saudi Journal of Biological Sciences. 2024, 31, 103944. https://doi.org/10.1016/j.sjbs.2024.103944
SCHMIDT, C., et al. Genetic diversity and IUCN Red List status. Conservation Biology. 2023, 37, e14064. https://doi.org/10.1111/cobi.14064
SINGH, H. P., RAIGAR, O. P., and CHAHOTA, R. K. Estimation of genetic diversity and its exploitation in plant breeding. The Botanical Review. 2022, 88, 413−435. https://doi.org/10.1007/s12229-021-09274-y
WAN, N. F., et al. Plant genetic diversity affects multiple trophic levels and trophic interactions. Nature Communications. 2022, 13, 7312. https://doi.org/10.1038/s41467-022-35087-7
WANG, F. G., et al. Principle and strategy of DNA fingerprint identification of plant variety. Molecular Plant Breeding. 2019, 10, 81–92. https://doi.org/10.5376/mpb.2019.10.0011
WANG, X. Y. Biological characteristics and cultivation techniques of Chinese Acer truncatum. Beijing: China Forestry Publishing House, 2019.
WANG, Y. Q., et al. Study on the variation of functional traits and environmental driving factors of different species origins of Acer truncatum in the Horqin Sandy Land. Acta Botanica Boreali-Occidentalia Sinica. 2024, 44, 300−309. https://doi.org/10.7606/j.issn.1000-4025.20230535
ZANG, Z. R., et al. Analysis of genetic diversity of Acer truncatum germplasm resources by fluorescent SSR markers. Molecular Plant Breeding. 2023, 21, 8162−8171. https://doi.org/10.13271/j.mpb.021.008163
ZHANG, H., et al. Development of SLAF-sequence and multiplex SNaPshot panels for population genetic diversity analysis and construction of DNA fingerprints for sugarcane. Genes. 2022, 13, 1477. https://doi.org/10.3390/genes13081477
ZHANG, J., et al. Genetic diversity analysis and variety identification using SSR and SNP markers in melon. BMC Plant Biology. 2023a, 23, 39. https://doi.org/10.1186/s12870-023-04056-7
ZHANG, M. M., et al. Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers. Scientific Reports. 2023b, 13, 19315. https://doi.org/10.1038/s41598-023-46798-2
ZHANG, P., et al. The brief study on the change of flora sex of Acer truncatum. Journal of Agriculture, 2014, 1, 41–44. https://doi.org/10.3969/j.issn.1007-7774.2014.04.009
ZHANG, X. Y., et al. A new utilization of total flavonoids from Acer truncatum samara and leaves: Anti-aging and metabolic regulation. Industrial Crops and Products. 2023c, 203, 117207. https://doi.org/10.1016/j.indcrop.2023.117207
ZHU, Y. X., et al. SSR molecular marker developments and genetic diversity analysis of Zanthoxylum nitidum (Roxb.) DC. Scientific Reports. 2023, 13, 20767. https://doi.org/10.1038/s41598-023-48022-7
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Zhiping Wu, Xuefang Wang, Minghai Han, Chi Zhang, Jun Wang, Hasengaowa Bao

This work is licensed under a Creative Commons Attribution 4.0 International License.