A Review of Molecular Marker Techniques used in Improving the Identification and Selection of Coconut (Cocos nucifera L.) Cultivars
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Abstract
The identification of plants using molecular biology and biotechnology is a recent development in genetics that enables efficient characterization. Past developments have emphasized advances in molecular marker technology, which has broad applications, including plant breeding and basic plant research. The development of various techniques is essential in determining genetic diversity. These include PCR-based markers like the amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSRs), single nucleotide polymorphism (SNP), expressed sequence tag (EST), inter simple sequence repeats (ISSR); hybridisation-based markers like the restriction fragment length polymorphism (RFLP); and biochemical markers like the proteins (isozymes and allozymes) and phytochemicals (secondary metabolites such as alkaloids, flavonoids, and terpenes). Some of these methods were applied to research on coconuts' genetic diversity. New approaches are continually being developed, but each has its limitations. None is suitable for meeting all the expectations placed by the researchers. This overview provides the basic principles, requirements, and limitations of several widely used DNA marker techniques that may be applied to general studies of coconut genetic diversity.
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References
Rajesh, M. K.; Ramesh, S. V.; Perera, L.; Manickavelu, A. Quantitative Trait Loci (QTL) and Association Mapping for Major Agronomic Traits. In The Coconut Genome; Springer International Publishing: Cham, Switzerland, 2021. https://doi.org/10.1007/978-3-030-76649-8_6.
Prades, A.; Salum, U. N.; Pioch, D. Oil Crops and the Supply Chain in Asia: New Era for the Coconut Sector. OCL 2016, 23(6), D606. https://doi.org/10.1051/ocl/2016048.
Belkhadir, Y.; Subramaniam, R.; Dangl, J. L. Plant Disease Resistance Protein Signalling: NBS-LRR Proteins and Their Partners. Curr. Opin. Plant Biol. 2004, 7(4), 391–399. https://doi.org/10.1016/j.pbi.2004.05.009
Nampoothiri, K. U. K.; Krishnakumar, V.; Thampan, P. K.; Achuthan Nair, M. The Coconut Palm (Cocos nucifera L.): Research and Development Perspectives; Springer: Singapore, 2019. https://doi.org/10.1007/978-981-13-2754-4
Amiteye, S. Basic Concepts and Methodologies of DNA Marker Systems in Plant Molecular Breeding. Heliyon 2021, 7(10), e08093. https://doi.org/10.1016/j.heliyon.2021.e08093
Lucht, J. M. Public Acceptance of Plant Biotechnology and GM Crops. Viruses 2015, 7(8), 4254–4281. https://doi.org/10.3390/v7082819
Arti, D.; Sharma, K.; Khar, S. Molecular Markers: Role in Plant Sciences. J. Pharmacogn. Phytochem. 2020.
Jerard, B. A.; Samsudeen, K.; Preethi, P.; Rajesh, M. K.; Karun, A. Identification and Utilisation of Informative EST-SSR Markers for Genetic Purity Testing of Coconut Hybrids. J. Plant. Crops 2016, 44(2), 77–84. https://doi.org/10.19071/jpc.2016.v44.i2.3101
Collard, B. C. Y.; Jahufer, M. Z. Z.; Brouwer, J. B.; Pang, E. C. K. An Introduction to Markers, Quantitative Trait Loci (QTL) Mapping and Marker-Assisted Selection for Crop Improvement: The Basic Concepts. Euphytica 2005, 142(1–2), 169–196. https://doi.org/10.1007/s10681-005-1681-5
Kumar, M.; Patel, S. V.; Chaudhary, V.; Sirohi, U.; Singh, J.; Sharma, R.; Kumar, C. M. Advances in Biochemical and Molecular Marker Techniques and Their Applications in Genetic Studies of Orchids: A Review. Int. J. Chem. Stud. 2018, 6(6), 806–822.
Xu, Y. Molecular Plant Breeding; CABI: Wallingford, U.K., 2010. https://doi.org/10.1079/9781845933920.0000
Hailu, G.; Asfere, Y. The Role of Molecular Markers in Crop Improvement and Plant Breeding Programs: A Review. Agric. J. 2020, 15(6), 171–175.
Emrey, T. M. Application of Molecular Markers SNP and DArT in Plant Breeding: A Review. J. Agric. Crops 2018, 4(8), 86–92.
Botstein, D.; White, R. L.; Skolnick, M.; Davis, R. W. Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms. Am. J. Hum. Genet. 1980, 32, 314–331.
Jones, N.; Ougham, H.; Thomas, H.; Pašakinskienė, I. Markers and Mapping Revisited: Finding Your Gene. New Phytol. 2009, 183(4), 935–966. https://doi.org/10.1111/j.1469-8137.2009.02933.x
Jiang, G. L. Molecular Markers and Marker-Assisted Breeding in Plants. In Plant Breeding from Laboratories to Fields; Andersen, S. B., Ed.; IntechOpen: London, U.K., 2013; pp 45–83. https://doi.org/10.5772/52583
Teulat, B.; Aldam, C.; Trehin, R.; Lebrun, P.; Barker, J. H. A.; Arnold, G. M.; Karp, A.; Baudouin, L.; Rognon, F. An Analysis of Genetic Diversity in Coconut (Cocos nucifera L.) Populations from across the Geographic Range Using Sequence-Tagged Microsatellites (SSRs) and AFLPs. Theor. Appl. Genet. 2000, 100(5), 764–771. https://doi.org/10.1007/s001220051350
Tanksley, S. D.; Young, N. D.; Paterson, A. H.; Bonierbale, M. W. RFLP Mapping in Plant Breeding: New Tools for an Old Science. Bio/Technology 1989, 7(3), 257–264. https://doi.org/10.1038/nbt0389-257
Ashburner, G. R. The Application of Molecular Markers to Coconut Genetic Improvement. In Physiology of Tropical Crops; Springer, 1999; pp 33–44. https://doi.org/10.1007/978-94-015-9283-3_3
Southern, E. M. Detection of Specific Sequences among DNA Fragments Separated by Gel Electrophoresis. J. Mol. Biol. 1975, 98(3), 503–517. https://doi.org/10.1016/S0022-2836(75)80083-0
Kundan, M. K.; Vinita, T.; Yachana, J.; Madhumati, B. Potential and Application of Molecular Marker Techniques for Plant Genome Analysis. Int. J. Pure Appl. Biosci. 2014, 2(1), 169–188.
Lateef, D. D. DNA Marker Technologies in Plants and Applications for Crop Improvements. J. Biosci. Med. 2015, 3(5), 7–18. https://doi.org/10.4236/jbm.2015.35002
Welsh, J.; McClelland, M. Fingerprinting Genomes Using PCR with Arbitrary Primers. Nucleic Acids Res. 1990, 18(24), 7213–7218. https://doi.org/10.1093/nar/18.24.7213.
Ramesh, P.; Mallikarjuna, G.; Sameena, S.; Kumar, A.; Gurulakshmi, K.; Reddy, B. V.; Reddy, P. C. O.; Sekhar, A. C. Advancements in Molecular Marker Technologies and Their Applications in Diversity Studies. J. Biosci. 2020, 45, 89. https://doi.org/10.1007/s12038-020-00089-4
Upadhyay, A.; Jayadev, K.; Manimekalai, R.; Parthasarathy, V. A. Genetic Relationship and Diversity in Indian Coconut Accessions Based on RAPD Markers. Sci. Hortic. 2004, 99(3–4), 353–362. https://doi.org/10.1016/S0304-4238(03)00103-1
Cardeña, R.; Ashburner, G. R.; Oropeza, C. Identification of RAPDs Associated with Resistance to Lethal Yellowing of the Coconut (Cocos nucifera L.) Palm. Sci. Hortic. 2003, 98(3), 257–263. https://doi.org/10.1016/S0304-4238(02)00162-0
Manimekalai, R.; Nagarajan, P. Interrelationships among Coconut (Cocos nucifera L.) Accessions Using RAPD Technique. Genet. Resour. Crop Evol. 2006, 53(6), 1137–1144. https://doi.org/10.1007/s10722-005-1303-z
Ho, V. T.; Ngo, T. K. A.; Phan, T. H. T.; Ta, T. T. T.; Tran, T. K. P. Genetic Diversity among Passion Fruit (Passiflora edulis) Accessions of Southern Vietnam Using RAPD and ISSR Markers. SABRAO J. Breed. Genet. 2021, 53(1), 1–14.
Tilwari, A.; Sharma, R. Random Amplified Polymorphic DNA and Inter-Simple Sequence Repeat Markers Reveal Genetic Diversity among Micropropagated, Wild, and Field-Cultivated Genotypes of Gloriosa superba. Mol. Biol. Rep. 2021, 48(3), 2437–2452. https://doi.org/10.1007/s11033-021-06278-0
Ashburner, G. R.; Thompson, W. K.; Halloran, G. M. RAPD Analysis of South Pacific Coconut Palm Populations. Crop Sci. 1997, 37(3), 992–997. https://doi.org/10.2135/cropsci1997.0011183X003700030048x
Jones, C. J.; Edwards, K. J.; Castaglione, S.; Winfield, M. O.; Sala, F.; Van de Wiel, C.; Bredemeijer, G.; Vosman, B.; Matthes, M.; Daly, A.; Karp, A. Reproducibility Testing of RAPD, AFLP and SSR Markers in Plants by a Network of European Laboratories. Mol. Breed. 1997, 3(5), 381–390. https://doi.org/10.1023/A:1009612517139
Nartvaranant, P. Genetic Variations for Nam Hom Coconut (Cocos nucifera L.) Grown in the Western Region of Thailand Using AFLP Markers. J. Thai Interdiscip. Res. 2019, 14(1), 12–20. https://doi.org/10.14456/jtir.2019.3
Kalia, R. K.; Rai, M. K.; Kalia, S.; Singh, R.; Dhawan, A. K. Microsatellite Markers: An Overview of the Recent Progress in Plants. Euphytica 2011, 177(3), 309–334. https://doi.org/10.1007/s10681-010-0286-9
Dunn, G.; Hinrichs, A. L.; Bertelsen, S.; Jin, C. H.; Kauwe, J. S. K.; Suarez, B. K.; Bierut, L. J. Microsatellites versus Single-Nucleotide Polymorphisms in Linkage Analysis for Quantitative and Qualitative Measures. BMC Genet. 2005, 6(Suppl. 1), S122. https://doi.org/10.1186/1471-2156-6-S1-S122
McGregor, C. E.; Lambert, C. A.; Greyling, M. M.; Louw, J. H.; Warnich, L. A Comparative Assessment of DNA Fingerprinting Techniques (RAPD, ISSR, AFLP and SSR) in Tetraploid Potato (Solanum tuberosum L.) Germplasm. Euphytica 2000, 113(2), 135–144. https://doi.org/10.1023/A:1003925620546
Caro, R. E. S.; Cagayan, J.; Gardoce, R. R.; Manohar, A. N. C.; Canama-Salinas, A. O.; Rivera, R. L.; Lantican, D. V.; Galvez, H. F.; Reaño, C. E. Mining and Validation of Novel Simple Sequence Repeat (SSR) Markers Derived from the Coconut (Cocos nucifera L.) Genome Assembly. J. Genet. Eng. Biotechnol. 2022, 20(1), 113. https://doi.org/10.1186/s43141-022-00354-z
Perera, L.; Russell, J. R.; Provan, J.; Powell, W. Use of Microsatellite DNA Markers to Investigate the Level of Genetic Diversity and Population Genetic Structure of Coconut (Cocos nucifera L.). Genome 2000, 43(1), 15–21. https://doi.org/10.1139/gen-43-1-15
Perera, L.; Russell, J. R.; Provan, J.; Powell, W. Levels and Distribution of Genetic Diversity of Coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka Assessed by Microsatellite Markers. Euphytica 2001, 122, 381–389. https://doi.org/10.1023/A:1012987224319
Lebrun, P.; Berger, A.; Hodgkin, T.; Baudouin, L. Biochemical and Molecular Methods for Characterising Coconut Diversity. In Coconut Genetic Resources; IPGRI: Rome, Italy, 2005; pp 225–245.
Konan, K. J. N.; Koffi, K. E.; Konan, J. L.; Lebrun, P.; Dery, S. K.; Sangare, A. Microsatellite Gene Diversity in Coconut (Cocos nucifera L.) Accessions Resistant to Lethal Yellowing Disease. Afr. J. Biotechnol. 2007, 6(4), 341–347.
Ribeiro, F. E.; Baudouin, L.; Lebrun, P.; Chaves, L. J.; Brondani, C.; Zucchi, M. I.; Vencovsky, R. Population Structures of Brazilian Tall Coconut (Cocos nucifera L.) by Microsatellite Markers. Genet. Mol. Biol. 2010, 33(4), 696–702. https://doi.org/10.1590/S1415-47572010005000077
Rajesh, M. K.; Nagarajan, P.; Jerard, B. A.; Arunachalam, V.; Dhanapal, R. Microsatellite Variability of Coconut Accessions (Cocos nucifera L.) from Andaman and Nicobar Islands. Curr. Sci. 2008, 94(12), 1627–1631.
Meerow, A. W.; Wisser, R. J.; Brown, J. S.; Kuhn, D. N.; Schnell, R. J.; Broschat, T. K. Analysis of Genetic Diversity and Population Structure within Florida Coconut (Cocos nucifera L.) Germplasm Using Microsatellite DNA, with Special Emphasis on the Fiji Dwarf Cultivar. Theor. Appl. Genet. 2003, 106(4), 715–726. https://doi.org/10.1007/s00122-002-1121-z
Geethanjali, S.; Anitha Rukmani, J.; Rajakumar, D.; Kadirvel, P.; Viswanathan, P. L. Genetic Diversity, Population Structure and Association Analysis in Coconut (Cocos nucifera L.) Germplasm Using SSR Markers. Plant Genet. Resour. 2018, 16(2), 156–168. https://doi.org/10.1017/S1479262117000119
Rahayu, M. S.; Setiawan, A.; Maskromo, I.; Purwito, A.; Sudarsono. Genetic Diversity Analysis of Puan Kalianda Kopyor Coconuts (Cocos nucifera L.) Based on SSR Markers. Biodiversitas 2022, 23(1), 205–211. https://doi.org/10.13057/biodiv/d230126
Keawsaard, Y.; Pentem, P.; Rotduang, P.; Weeraphong, M.; Ramasoot, S. Induction of Mutation in Toothbrush Orchids Using Ethyl Methane Sulphonate (EMS) and Detection of Genetic Variation by SSR (Simple Sequence Repeat) Marker. ASEAN J. Sci. Technol. Rep. 2025, 28(1), e255125. https://doi.org/10.55164/ajstr.v28i1.255125
Luces, H. C. A Bibliometric Analysis of Stress Memory and Priming in Plants: Research Trends, Mechanisms, and Implications for Agricultural Resilience. ASEAN J. Sci. Technol. Rep. 2025, 29(1), e259013. https://doi.org/10.55164/ajstr.v29i1.259013
Pothipongsa, A.; Damsud, T.; Burut-Archanai, S. Molecular Docking of Bioactive Compounds from Thai Medicinal Plants against Xanthine Oxidase for Gout Treatment. ASEAN J. Sci. Technol. Rep. 2024, 27(1), e250948. https://doi.org/10.55164/ajstr.v27i1.250948
Nayan, M. A. N.; Sarizan, M. N.; Mackeen, M. M. M. Carbohydrate Interfaces in Plant–Fungal Interactions: A Scoping Review. ASEAN J. Sci. Technol. Rep. 2026, 29(5), e260552. https://doi.org/10.55164/ajstr.v29i5.262552
Nadeem, M. A.; Nawaz, M. A.; Shahid, M. Q.; Doğan, Y.; Comertpay, G.; Yıldız, M.; Hatipoğlu, R.; Ahmad, F.; Alsaleh, A.; Labhane, N.; Özkan, H.; Chung, G.; Baloch, F. S. DNA Molecular Markers in Plant Breeding: Current Status and Recent Advancements in Genomic Selection and Genome Editing. Biotechnol. Biotechnol. Equip. 2018, 32(2), 261–285. https://doi.org/10.1080/13102818.2017.1400401
Zietkiewicz, E.; Rafalski, A.; Labuda, D. Genome Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification. Genomics 1994, 20(2), 176–183. https://doi.org/10.1006/geno.1994.1151
Sharafi, A. A.; Abkenar, A. A.; Sharafi, A. Molecular Genetic Diversity Assessment of Citrus Species Grown in Iran Revealed by SSR, ISSR and CAPS Molecular Markers. J. Sci. Res. 2017, 2(8), 22–27. https://doi.org/10.26910/issn.2528-8083vol2iss8.2017pp22-27
Yadav, A.; Kothari, S. L.; Kachhwaha, S.; Joshi, A. In Vitro Propagation of Chia (Salvia hispanica L.) and Assessment of Genetic Fidelity Using RAPD and ISSR Molecular Markers. J. Appl. Biol. Biotechnol. 2019, 7(1), 42–47. https://doi.org/10.7324/JABB.2019.70108
Zizumbo-Villarreal, D.; Ruiz-Rodríguez, M.; Harries, H.; Colunga-García Marín, P. Population Genetics, Lethal Yellowing Disease, and Relationships among Mexican and Imported Coconut Ecotypes. Crop Sci. 2006, 46(6), 2509–2516. https://doi.org/10.2135/cropsci2005.12-0462
Rasam, D. V.; Gokhale, N. B.; Sawardekar, S. V.; Patil, D. M. Molecular Characterisation of Coconut (Cocos nucifera L.) Varieties Using ISSR and SSR Markers. J. Hortic. Sci. Biotechnol. 2016, 91(4), 347–352. https://doi.org/10.1080/14620316.2016.1160544
Loiola, C. M.; Azevedo, A. O. N.; Diniz, L. E. C.; Aragão, W. M.; Carlos, C. D.; Santos, P. H. A. D.; Ramos, H. C. C.; Pereira, M. G.; Ramos, S. R. R. Genetic Relationships among Tall Coconut Palm (Cocos nucifera L.) Accessions of the International Coconut Genebank for Latin America and the Caribbean (ICG-LAC) Evaluated Using Microsatellite Markers (SSRs). PLoS One 2016, 11(3), e0151309. https://doi.org/10.1371/journal.pone.0151309
Nouri, A.; Golabadi, M.; Etminan, A.; Rezaei, A.; Mehrabi, A. A. Comparative Assessment of SCoT and ISSR Markers for Analysis of Genetic Diversity and Population Structure in Some Aegilops tauschii Accessions. Plant Genet. Resour. 2021, 19(5), 375–383. https://doi.org/10.1017/S147926212100040X
Thakur, J.; Dwivedi, M. D.; Sourabh, P.; Uniyal, P. L.; Pandey, A. K. Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micro-Propagated Pittosporum eriocarpum Royle. PLoS One 2016, 11(7), e0159050. https://doi.org/10.1371/journal.pone.0159050
Huang, X.; Yang, L.; Jin, Y.; Lin, J.; Liu, F. Generation, Annotation, and Analysis of a Large-Scale Expressed Sequence Tag Library from Arabidopsis pumila to Explore Salt-Responsive Genes. Front. Plant Sci. 2017, 8, 955. https://doi.org/10.3389/fpls.2017.00955
Bang, K. H.; Lee, J. W.; Kim, Y. C.; Kim, D. H.; Lee, E. H.; Jeung, J. U. Construction of a Genomic DNA Library of Korean Ginseng (Panax ginseng) and Development of Sequence-Tagged Sites. Biol. Pharm. Bull. 2010, 33(9), 1579–1588. https://doi.org/10.1248/bpb.33.1579
Reddy, A. R.; Ramakrishna, W.; Sekhar, A. C.; Ithal, N.; Babu, P. R.; Bonaldo, M. F.; Soares, M. B.; Bennetzen, J. L. Novel Genes Are Enriched in Normalized cDNA Libraries from Drought-Stressed Seedlings of Rice (Oryza sativa L.). Genome 2002, 45(1), 204–211. https://doi.org/10.1139/g01-114
Xiao, N.; Wang, H.; Yao, W.; Zhang, M.; Ming, R.; Zhang, J. Development and Evaluation of SSR Markers Based on Large-Scale Full-Length Transcriptome Sequencing in Sugarcane. Trop. Plant Biol. 2020, 13(4), 343–352. https://doi.org/10.1007/s12042-020-09260-5
Bushakra, J. M.; Lewers, K. S.; Staton, M. E.; Zhebentyayeva, T.; Saski, C. A. Developing Expressed Sequence Tag Libraries and the Discovery of Simple Sequence Repeat Markers for Two Species of Raspberry (Rubus L.). BMC Plant Biol. 2015, 15(1), 258. https://doi.org/10.1186/s12870-015-0629-8
Preethi, P.; Rahman, S.; Naganeeswaran, S.; Sabana, A. A.; Gangaraj, K. P.; Jerard, B. A.; Niral, V.; Rajesh, M. K. Development of EST-SSR Markers for Genetic Diversity Analysis in Coconut (Cocos nucifera L.). Mol. Biol. Rep. 2020, 47(12), 9385–9397. https://doi.org/10.1007/s11033-020-05981-8
Manivannan, A.; Choi, S.; Jun, T. H.; Yang, E. Y.; Kim, J. H.; Lee, E. S.; Lee, H. E.; Kim, D. S.; Ahn, Y. K. Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait. Biomed Res. Int. 2021, 2021, 6673010. https://doi.org/10.1155/2021/6673010
Fusari, C. M.; Lia, V. V.; Hopp, H. E.; Heinz, R. A.; Paniego, N. B. Identification of Single-Nucleotide Polymorphisms and Analysis of Linkage Disequilibrium in Sunflower Elite Inbred Lines Using the Candidate-Gene Approach. BMC Plant Biol. 2008, 8, 7. https://doi.org/10.1186/1471-2229-8-7
Bai, B.; Wang, L.; Zhang, Y. J.; Lee, M.; Rahmadsyah, R.; Alfiko, Y.; Purwantomo, S.; Suwanto, A.; Chua, N. H.; Yue, G. H. Developing Genome-Wide SNPs and Constructing an Ultrahigh-Density Linkage Map in Oil Palm. Sci. Rep. 2018, 8(1), 691. https://doi.org/10.1038/s41598-017-18613-2
Muñoz-Pérez, J. M.; Cañas, G. P.; López, L.; Arias, T. Genome-Wide Diversity Analysis to Infer Population Structure and Linkage Disequilibrium among Colombian Coconut Germplasm. Sci. Rep. 2022, 12(1), 3188. https://doi.org/10.1038/s41598-022-07013-w
Mauro-Herrera, M.; Meerow, A. W.; Borrone, J. W.; Kuhn, D. N.; Schnell, R. J. Ten Informative Markers Developed from WRKY Sequences in Coconut (Cocos nucifera L.). Mol. Ecol. Notes 2006, 6(3), 904–906. https://doi.org/10.1111/j.1471-8286.2006.01393.x
Chen, Z.; Wang, G.; Li, M.; Peng, Z.; Ali, H.; Xu, L.; Gurr, G. M.; Hou, Y. Development of Single-Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure in Coconut Leaf Beetle. Insects 2020, 11(4), 230. https://doi.org/10.3390/insects11040230
Santos, P. H. A. D.; Venâncio, T. M.; Ramos, H. C. C.; Arêdes, F. A. S.; Azevedo, A. O. N.; Boechat, M. S. B.; de Souza Filho, G. A.; Ramos, S. R. R.; Mirisola, L. A.; Aragão, W. M.; Pereira, M. G. Genotyping-by-Sequencing Technology Reveals Directions for Coconut (Cocos nucifera L.) Breeding Strategies for Water Production. Euphytica 2020, 216(3), 44. https://doi.org/10.1007/s10681-020-02582-1
