Advancements in DNA-based molecular markers to unravel the genetic diversity of endangered plants
DOI:
https://doi.org/10.25081/cb.2025.v16.9010Keywords:
Genetic diversity, Endangered plants, Molecular markersAbstract
One of the primary requirements to develop effective and practical sustainable management strategies for endangered plant species, is the assessment of genetic diversity. DNA-based molecular markers have proven themselves to be an excellent tool to assess many parameters including elucidation of genetic diversity for the past few decades. During this period, DNA-based marker technology has undergone many changes. From the initial RFLP to the contemporary systems that use high-throughput sequencing or next-generation sequencing platforms that have revolutionized genetic diversity assessment. This review focuses on the application of the molecular markers and, a few of their variants, to evaluate the genetic diversity of endangered plants along with their advantages, limitations as well as future prospects and scope.
Downloads
References
Aiello, D., Ferradini, N., Torelli, L., Volpi, C., Lambalk, J., Russi, L., & Albertini, E. (2020). Evaluation of cross-species transferability of SSR markers in Foeniculum vulgare. Plants, 9(2), 175. https://doi.org/10.3390/plants9020175
Aldaba Núñez, F. A., Veltjen, E., Martínez Salas, E. M., & Samain, M.-S. (2021). Disentangling Species Delineation and Guiding Conservation of Endangered Magnolias in Veracruz, Mexico. Plants, 10(4), 673. https://doi.org/10.3390/plants10040673
Alves, S. I. A., Dantas, C. W. D., Macedo, D. B., & Ramos, R. T. J. (2024). What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools. Frontiers in Genetics, 15, 1474611. https://doi.org/10.3389/fgene.2024.1474611
Bobo-Pinilla, J., Peñas de Giles, J., López-González, N., Mediavilla, S., & Martínez-Ortega, M. M. (2018). Phylogeography of an endangered disjunct herb: Long-distance dispersal, refugia and colonization routes. AoB Plants, 10(5), ply047. https://doi.org/10.1093/aobpla/ply047
Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314-331.
Caetano-Anollés, G., & Gresshoff, P. M. (1994). DNA amplification fingerprinting using arbitrary mini-hairpin oligonucleotide primers. Bio/Technology, 12, 619-623. https://doi.org/10.1038/nbt0694-619
Caetano-Anollés, G., Bassam, B. J., & Gresshoff, P. M. (1991). DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology, 9, 553-557. https://doi.org/10.1038/nbt0691-553
Cardle, L., Ramsay, L., Milbourne, D., Macaulay, M., Marshall, D., & Waugh, R. (2000). Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 156(2), 847-854. https://doi.org/10.1093/genetics/156.2.847
Chee-Sanford, J. C., & Connor, L. M. (2023). Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. PloS One, 18(11), e0294966. https://doi.org/10.1371/journal.pone.0294966
Cheng, J., Kao, H., & Dong, S. (2020). Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC Plant Biology, 20, 391. https://doi.org/10.1186/s12870-020-02594-y
Gai, Z., Zhai, J., Chen, X., Jiao, P., Zhang, S., Sun, J., Qin, R., Liu, H., Wu, Z., & Li, Z. (2021). Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China. Frontiers in Plant Science, 12, 705083. https://doi.org/10.3389/fpls.2021.705083
Garcia, C. B., Silva, A. V. da, Carvalho, I. A. S. de, Nascimento, W. F. do, Ramos, S. L. F., Rodrigues, D. P., Zucchi, M. I., Costa, F. M., Alves-Pereira, A., Batista, C. E. de A., Amaral, D. D., & Veasey, E. A. (2024). Low Diversity and High Genetic Structure for Platonia insignis Mart., an Endangered Fruit Tree Species. Plants, 13(7), 1033. https://doi.org/10.3390/plants13071033
Geethanjali, S., Kadirvel, P., Anumalla, M., Sadhana, N. H., Annamalai, A., & Ali, J. (2024). Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning. Plants, 13(18), 2619. https://doi.org/10.3390/plants13182619
Haque, I., Bandopadhyay, R., & Mukhopadhyay, K. (2010). Population genetic structure of the endangered and endemic medicinal plant Commiphora wightii. Molecular Biology Reports, 37, 847-854. https://doi.org/10.1007/s11033-009-9661-9
He, J., Zhao, X., Laroche, A., Lu, Z.-X., Liu, H., & Li, Z. (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science, 5, 484. https://doi.org/10.3389/fpls.2014.00484
Hosseini, M. S., Ebrahimi, M., Samsampour, D., Abadía, J., Khanahmadi, M., Amirian, R., Ghafoori, I. N., Ghaderi-Zefrehei, M., & Gogorcena, Y. (2021). Association analysis and molecular tagging of phytochemicals in the endangered medicinal plant licorice (Glycyrrhiza glabra L.). Phytochemistry, 183, 112629. https://doi.org/10.1016/j.phytochem.2020.112629
Hu, S., Wang, M., Yan, X., & Cheng, X. (2024). Genetic Diversity and Population Structure of Endangered Orchid Cypripedium flavum in Fragmented Habitat Using Fluorescent AFLP Markers. Plants, 13(20), 2851. https://doi.org/10.3390/plants13202851
Huang, P.-H., Wang, T.-R., Li, M., Fang, O.-Y., Su, R.-P., Meng, H.-H., Song, Y.-G., & Li, J. (2024). Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes. Plant Science, 344, 112109. https://doi.org/10.1016/j.plantsci.2024.112109
Jacquemart, A.-L., Buyens, C., Delescaille, L.-M., & Van Rossum, F. (2021). Using genetic evaluation to guide conservation of remnant Juniperus communis (Cupressaceae) populations. Plant Biology, 23(1), 193-204. https://doi.org/10.1111/plb.13188
Jiang, Y., Xu, S., Wang, R., Zhou, J., Dou, J., Yin, Q., & Wang, R. (2020). Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species. BMC Plant Biology, 20, 522. https://doi.org/10.1186/s12870-020-02727-3
Kapoor, B., Kumar, A., & Kumar, P. (2021). Transcriptome repository of North-Western Himalayan endangered medicinal herbs: A paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. Molecular Genetics and Genomics, 296, 1177-1202. https://doi.org/10.1007/s00438-021-01821-x
Kochert, G. (1991). Restriction fragment length polymorphism in plants and its implications. In B. B. Biswas & J. R. Harris (Eds.), Sub-Cellular Biochemistry (Vol. 17, pp. 167-190) New York, US: Springer. https://doi.org/10.1007/978-1-4613-9365-8_8
Kumar, A., Rajpal, V. R., Ambika, Devarumath, R. M., Kumari, A., Thakur, R., Chaudhary, M., Singh, P. P., Chauhan, S. M. S., & Raina, S. N. (2021a). Isolation and HPLC assisted quantification of two iridoid glycoside compounds and molecular DNA fingerprinting in critically endangered medicinal Picrorhiza kurroa Royle ex Benth: Implications for conservation. Physiology and Molecular Biology of Plants, 27, 727-746. https://doi.org/10.1007/s12298-021-00972-w
Kumar, P., Choudhary, M., Jat, B. S., Kumar, B., Singh, V., Kumar, V., Singla, D., & Rakshit, S. (2021b). Skim sequencing: an advanced NGS technology for crop improvement. Journal of Genetics, 100, 38. https://doi.org/10.1007/s12041-021-01285-3
Lasky, J. R., Josephs, E. B., & Morris, G. P. (2023). Genotype-environment associations to reveal the molecular basis of environmental adaptation. The Plant Cell, 35(1), 125-138. https://doi.org/10.1093/plcell/koac267
Li, A., Ma, M., Li, H., He, S., & Wang, S. (2023). Genetic Diversity and Population Differentiation of a Chinese Endangered Plant Ammopiptanthus nanus (M. Pop.) Cheng f.. Genes, 14(5), 1020. https://doi.org/10.3390/genes14051020
Li, X., Liu, X., Wei, J., Li, Y., Tigabu, M., & Zhao, X. (2020). Development and Transferability of EST-SSR Markers for Pinus koraiensis from Cold-Stressed Transcriptome through Illumina Sequencing. Genes, 11(5), 500. https://doi.org/10.3390/genes11050500
Mafakheri, M., Bakhshipour, M., Omrani, M., Gholizadeh, H., Rahimi, N., Mobaraki, A., & Rahimi, M. (2022). The impact of environmental and climatic variables on genetic diversity and plant functional traits of the endangered tuberous orchid (Orchis mascula L.). Scientific Reports, 12, 19765. https://doi.org/10.1038/s41598-022-19864-4
Mahdavikia, F., Ebadi, M.-T., Shojaeiyan, A., Ayyari, M., & Falahati-Anbaran, M. (2024). Genetic variation and structure of endemic and endangered wild celery (Kelussia odoratissima Mozaff.) quantified using novel microsatellite markers developed by next-generation sequencing. Frontiers in Plant Science, 15, 1301936. https://doi.org/10.3389/fpls.2024.1301936
Malkócs, T., Laczkó, L., Bereczki, J., Meglécz, E., Szövényi, P., & Sramkó, G. (2020). Development and characterization of novel SSR markers in the endangered endemic species Ferula sadleriana. Applications in Plant Sciences, 8(2), e11321. https://doi.org/10.1002/aps3.11321
Meyer, W., Mitchell, T. G., Freedman, E. Z., & Vilgalys, R. (1993). Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. Journal of Clinical Microbiology, 31(9), 2274-2280. https://doi.org/10.1128/jcm.31.9.2274-2280.1993
Nygaard, M., Kopatz, A., Speed, J. M. D., Martin, M. D., Prestø, T., Kleven, O., & Bendiksby, M. (2022). Spatiotemporal monitoring of the rare northern dragonhead (Dracocephalum ruyschiana, Lamiaceae) - SNP genotyping and environmental niche modeling herbarium specimens. Ecology and Evolution, 12(8), e9187. https://doi.org/10.1002/ece3.9187
Paliwal, R., Singh, R., Choudhury, D. R., Tiwari, G., Kumar, A., Bhat, K. C., & Singh, R. (2022). Molecular characterization of Tinospora cordifolia (Willd.) Miers using novel g-SSR markers and their comparison with EST-SSR and SCoT markers for genetic diversity Study. Genes, 13(11), 2042. https://doi.org/10.3390/genes13112042
Palumbo, F., Vannozzi, A., Vitulo, N., Lucchin, M., & Barcaccia, G. (2018). The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants. Scientific Reports, 8, 10459. https://doi.org/10.1038/s41598-018-28775-2
Penner, G. A., Lee, S. J., Bezte, L. J., & Ugali, E. (1996). Rapid RAPD screening of plant DNA using dot blot hybridization. Molecular Breeding, 2, 7-10. https://doi.org/10.1007/BF00171347
Salgotra, R. K., & Chauhan, B. S. (2023). Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources. Genes, 14(1), 174. https://doi.org/10.3390/genes14010174
Sharma, R., Patil, C., Majeed, J., Kumar, S., & Aggarwal, G. (2022). Next-generation sequencing in the biodiversity conservation of endangered medicinal plants. Environmental Science and Pollution Research International, 29, 73795-73808. https://doi.org/10.1007/s11356-022-22842-y
Skroch, P., & Nienhuis, J. (1995). Impact of scoring error and reproducibility RAPD data on RAPD based estimates of genetic distance. Theoretical and Applied Genetics, 91, 1086-1091. https://doi.org/10.1007/BF00223923
Teixeira, T. M., & Nazareno, A. G. (2021). One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species. Frontiers in Plant Science, 12, 730258. https://doi.org/10.3389/fpls.2021.730258
Ul Islam, S., Ahmed Mangral, Z., Tariq, L., Ahmad Bhat, B., Waseem Tantray, W., Ahmad, R., Ahmad Khuroo, A., & Ul Hassan Dar, T. (2023). Conservation genetics of endangered Trillium govanianum Wall. Ex D. Don - A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery. Gene, 888, 147748. https://doi.org/10.1016/j.gene.2023.147748
Van Rossum, F., & Godé, C. (2022). Development of highly polymorphic microsatellite markers for Campanula glomerata L. (Campanulaceae). Molecular Biology Reports, 49, 805-810. https://doi.org/10.1007/s11033-021-06839-3
Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., & Zabeau, M. (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23(21), 4407-4414. https://doi.org/10.1093/nar/23.21.4407
Vu, D. D., Shah, S. N. M., Pham, M. P., Bui, V. T., Nguyen, M. T., & Nguyen, T. P. T. (2020). De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC Plant Biology, 20, 358. https://doi.org/10.1186/s12870-020-02571-5
Wang, C., Ma, X., Ren, M., & Tang, L. (2020). Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China. PloS One, 15(11), e0241452. https://doi.org/10.1371/journal.pone.0241452
Wang, L., Yang, J., Zhang, H., Tao, Q., Zhang, Y., Dang, Z., Zhang, F., & Luo, Z. (2022). Sequence coverage required for accurate genotyping by sequencing in polyploid species. Molecular Ecology Resources, 22(4), 1417-1426. https://doi.org/10.1111/1755-0998.13558
Wang, T.-R., Meng, H.-H., Wang, N., Zheng, S.-S., Jiang, Y., Lin, D.-Q., Song, Y.-G., & Kozlowski, G. (2023). Adaptive divergence and genetic vulnerability of relict species under climate change: A case study of Pterocarya macroptera. Annals of Botany, 132(2), 241-254. https://doi.org/10.1093/aob/mcad083
Wiedenfeld, D. A., Alberts, A. C., Angulo, A., Bennett, E. L., Byers, O., Contreras-MacBeath, T., Drummond, G., da Fonseca, G. A. B., Gascon, C., Harrison, I., Heard, N., Hochkirch, A., Konstant, W., Langhammer, P. F., Langrand, O., Launay, F., Lebbin, D. J., Lieberman, S., Long, B., … Zhang, L. (2021). Conservation resource allocation, small population resiliency, and the fallacy of conservation triage. Conservation Biology, 35(5), 1388-1395. https://doi.org/10.1111/cobi.13696
Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18(22), 6531-6535. https://doi.org/10.1093/nar/18.22.6531
Yousefzadeh, H., Raeisi, S., Esmailzadeh, O., Jalali, G., Nasiri, M., Walas, Ł., & Kozlowski, G. (2021). Genetic Diversity and Structure of Rear Edge Populations of Sorbus aucuparia (Rosaceae) in the Hyrcanian Forest. Plants, 10(7), 1471. https://doi.org/10.3390/plants10071471
Yu, Y.-L., Wang, H.-C., Yu, Z.-X., Schinnerl, J., Tang, R., Geng, Y.-P., & Chen, G. (2021). Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River. Plant Diversity, 43(3), 225–233. https://doi.org/10.1016/j.pld.2020.12.007
Zhang, Y., Liu, X., Li, Y., Liu, X., Ma, H., Qu, S., & Li, Z. (2022). Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China. Plants, 11(9), 1204. https://doi.org/10.3390/plants11091204
Zhang, Y., Zhang, X., Wang, Y.-H., & Shen, S.-K. (2017). De Novo Assembly of Transcriptome and Development of Novel EST-SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing. Frontiers in Plant Science, 8, 1664. https://doi.org/10.3389/fpls.2017.01664
Zhao, R., He, Q., Chu, X., He, A., Zhang, Y., & Zhu, Z. (2024). Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China. Frontiers in Plant Science, 15, 1277173. https://doi.org/10.3389/fpls.2024.1277173
Zhao, Y., Zhang, J., Zhang, Z., & Xie, W. (2019). Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation. BMC Plant Biology, 19, 102. https://doi.org/10.1186/s12870-019-1691-4
Zhou, C., Xia, S., Wen, Q., Song, Y., Jia, Q., Wang, T., Liu, L., & Ouyang, T. (2023a). Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation. BMC Plant Biology, 23, 220. https://doi.org/10.1186/s12870-023-04231-w
Zhou, Y., Ye, Y., Zhu, G., Xu, Y., Tan, J., & Liu, J. (2023b). Diversity, classification, and EST-SSR-based association analysis of caladium ornamental traits. Physiologia Plantarum, 175(1), e13841. https://doi.org/10.1111/ppl.13841
Zhu, X., Zou, R., Qin, H., Chai, S., Tang, J., Li, Y., & Wei, X. (2023). Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis. Evolutionary Applications, 16(9), 1519-1530. https://doi.org/10.1111/eva.13584
Published
How to Cite
Issue
Section
Copyright (c) 2025 Inamul Haque
This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.
.