The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
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Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution melting (UP-HRM) marker is a useful tool for detecting of single nucleotide polymorphisms (SNPs). The objectives of this study were to develop UP-HRM markers to differentiate specific SNPs patterns on oil palm. The marker was developed and tested with Elaeis guineensis (Eg), Elaeis oleifera (Eo), Eo x Eg (hybrid), and was validated with 53 individuals of BC1F1 populations ((Eo x Eg) x Eg). Four UP-HRM markers were developed based on 2 SNPs in the stearoyl-acyl-carrier-protein 9-desaturase (EgSAD), 1 SNP in the auxin-responsive protein IAA27-like (EgIAA27), and 1 SNP in the 1-amino cyclopropane-1-carboxylate oxidase (EgACC) genes. The SNP discovery result showed that Eg was represented a reference homozygote genotype, while Eo was represented as an alternative homozygote genotype and the Eo x Eg hybrid was represented as a heterozygote genotype in all genes. The typical UP-HRM melt curve graph was successfully generated. This result was consistent with each genotype model for all four markers. The UP-HRM markers can distinguish each genotype according to the single-pass sequencing results. Furthermore, dendrogram analysis on validation divided 53 BC1F1 samples into three cluster groups.
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References
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Zhu, Yanfang, Qitian Wang, Jin Hu, Liwei Zhu, Jiancheng Wang, Shuijin Zhu, and Yajing Guan. 2013. “High Resolution Melting Curve Analysis?: An Efficient Method for Fingerprinting of Hybrid Rice Cultivars and Their Parental Lines.” Australian Journal of Crop Science 7 (13): 2048–53.
Chou, Lin, Shih Jie Huang, Chen Hsieh, Ming Te Lu, Chia Wei Song, and Fu Chiun Hsu. 2020. “A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (Prunus Persica) Chilling Requirement.” International Journal of Molecular Sciences 21 (4). https://doi.org/10.3390/ijms21041543.
Cobb, Joshua N, Partha S Biswas, and J Damien Platten. 2019. “Back to the Future?: Revisiting MAS as a Tool for Modern Plant Breeding.” Theoretical and Applied Genetics 132 (3): 647–67. https://doi.org/10.1007/s00122-018-3266-4.
Evanno, G., S. Regnaut, and J. Goudet. 2005. “Detecting the Number of Clusters of Individuals Using the Software STRUCTURE: A Simulation Study.” Molecular Ecology 14 (8): 2611–20. https://doi.org/10.1111/j.1365-294X.2005.02553.x.
Ganopoulos, Ioannis, Christos Bazakos, Panagiotis Madesis, Panagiotis Kalaitzis, and Athanasios Tsaftaris. 2013. “Barcode DNA High-Resolution Melting (Bar-HRM) Analysis as a Novel Close-Tubed and Accurate Tool for Olive Oil Forensic Use.” Journal of the Science of Food and Agriculture 93 (9): 2281–86. https://doi.org/10.1002/jsfa.6040.
Garritano, Sonia, Federica Gemignani, Catherine Voegele, Tú Nguyen-Dumont, Florence Le Calvez-Kelm, Deepika De Silva, Fabienne Lesueur, Stefano Landi, and Sean V. Tavtigian. 2009. “Determining the Effectiveness of High Resolution Melting Analysis for SNP Genotyping and Mutation Scanning at the TP53 Locus.” BMC Genetics 10: 1–12. https://doi.org/10.1186/1471-2156-10-5.
Ghatage, Tejaswini S, and Pulak Das. 2016. “High Resolution Melting Curve Analysis?: An Efficient Method for Genetic Purity Analysis of Cotton ( Gossypium Hirsutum ) Hybrid and Their Parental Lines” 2 (7): 49–53.
Kim, Ki-Seung, Daewoong Lee, Suk Bok Bae, Yong-Chul Kim, In-Soo Choi, Sun Tae Kim, Tae-Ho Lee, and Tae-Hwan Jun. 2017. “Development of SNP-Based Molecular Markers by Re-Sequencing Strategy in Peanut.” Plant Breeding and Biotechnology 5 (4): 325–33. https://doi.org/10.9787/PBB.2017.5.4.325.
Li, Shan, Songmei Liu, Yanhua Liu, Haiping Lu, Yuanyuan Tan, Jianzhong Huang, Pengcheng Wei, and Qing Yao Shu. 2018. “HRM-Facilitated Rapid Identification and Genotyping of Mutations Induced by CRISPR/ Cas9 Mutagenesis in Rice.” Crop Breeding and Applied Biotechnology 18 (2): 184–91. https://doi.org/10.1590/1984-70332018v18n2a26.
Lieveld, M., A. Carregosa, I. Benoy, N. Redzic, M. Berth, and D. Vanden Broeck. 2017. “A High Resolution Melting (HRM) Technology-Based Assay for Cost-Efficient Clinical Detection and Genotyping of Herpes Simplex Virus (HSV)-1 and HSV-2.” Journal of Virological Methods 248 (July): 181–86. https://doi.org/10.1016/j.jviromet.2017.07.005.
Lochlainn, Seosamh T., Stephen Amoah, Neil S. Graham, Khalid Alamer, Juan J. Rios, Smita Kurup, Andrew Stoute, et al. 2011. “High Resolution Melt (HRM) Analysis Is an Efficient Tool to Genotype EMS Mutants in Complex Crop Genomes.” Plant Methods 7 (1): 43. https://doi.org/10.1186/1746-4811-7-43.
Marshall, T. C., J. Slate, L. E.B. Kruuk, and J. M. Pemberton. 1998. “Statistical Confidence for Likelihood-Based Paternity Inference in Natural Populations.” Molecular Ecology 7 (5): 639–55. https://doi.org/10.1046/j.1365-294x.1998.00374.x.
Montgomery, Jesse L., Lindsay N. Sanford, and Carl T. Wittwer. 2010. “High-Resolution DNA Melting Analysis in Clinical Research and Diagnostics.” Expert Review of Molecular Diagnostics 10 (2): 219–40. https://doi.org/10.1586/erm.09.84.
Montoya, Carmenza, Benoit Cochard, Albert Flori, David Cros, Ricardo Lopes, Teresa Cuellar, Sandra Espeout, et al. 2014. “Genetic Architecture of Palm Oil Fatty Acid Composition in Cultivated Oil Palm (Elaeis Guineensis Jacq.) Compared to Its Wild Relative E. Oleifera (H.B.K) Cortés.” PLoS ONE 9 (5). https://doi.org/10.1371/journal.pone.0095412.
Montúfar, Rommel, Claude Louise, and Timothy Trabarger. 2018. “Elaeis Oleifera (Kunth) Cortés: A Neglected Palm from the Ecuadorian Amazon.” Revista Ecuatoriana de Medicina y Ciencias Biológicas 39 (1): 10–18. https://doi.org/10.26807/remcb.v39i1.584.
Ooi, Siew Eng, Chin Nee Choo, Zamzuri Ishak, and Meilina Ong-Abdullah. 2012. “A Candidate Auxin-Responsive Expression Marker Gene, EgIAA9, for Somatic Embryogenesis in Oil Palm (Elaeis Guineensis Jacq.).” Plant Cell, Tissue and Organ Culture 110 (2): 201–12. https://doi.org/10.1007/s11240-012-0143-8.
Pritchard, Jonathan K., Matthew Stephens, and Peter Donnelly. 2000. “Inference of Population Structure Using Multilocus Genotype Data.” Genetics 155 (2): 945–59.
Ririe, Kirk M., Randy P. Rasmussen, and Carl T. Wittwer. 1997. “Product Differentiation by Analysis of DNA Melting Curves during the Polymerase Chain Reaction.” Analytical Biochemistry 245 (2): 154–60. https://doi.org/10.1006/abio.1996.9916.
Ruskova, Lenka, and Vladislav Raclavsky. 2011. “The Potential of High Resolution Melting Analysis (HRMA) to Streamline, Facilitate and Enrich Routine Diagnostics in Medical Microbiology.” Biomedical Papers 155 (3): 239–52. https://doi.org/10.5507/bp.2011.045.
Saitou, Naruya, and Masatoshi Nei. 1987. “The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees.” Molecular Biology and Evolution 4 (4): 406–25. https://doi.org/10.1093/oxfordjournals.molbev.a040454.
Tranbarger, T. J., S. Dussert, T. Joet, X. Argout, M. Summo, A. Champion, D. Cros, A. Omore, B. Nouy, and F. Morcillo. 2011. “Regulatory Mechanisms Underlying Oil Palm Fruit Mesocarp Maturation, Ripening, and Functional Specialization in Lipid and Carotenoid Metabolism.” Plant Physiology 156 (2): 564–84. https://doi.org/10.1104/pp.111.175141.
Turnbull, N. cazemajor, M. Guerin, C. Louise, C. Amblard, P. Cochard, B. Durand-Gasselin, T. 2016. “Oil Palm Breeding and Seed Production in Africa Oil Palm Breeding and Seed Production in Africa.” Proceedings of the International Seminar on Oil Palm Breeding and Seed Production and Field Visits, no. September: 21–38. [Indonesian]
Zhang, Lina, Guanglin Cui, Zongzhe Li, Haoran Wang, Hu Ding, and Dao Wen Wang. 2013. “Comparison of High-Resolution Melting Analysis, Taqman Allelic Discrimination Assay, and Sanger Sequencing for Clopidogrel Efficacy Genotyping in Routine Molecular Diagnostics.” Journal of Molecular Diagnostics 15 (5): 600–606. https://doi.org/10.1016/j.jmoldx.2013.04.005.
Zhou, Luming, Ying Wang, and Carl T. Wittwer. 2011. “Rare Allele Enrichment and Detection by Allele-Specific PCR, Competitive Probe Blocking, and Melting Analysis.” BioTechniques 50 (5): 311–18. https://doi.org/10.2144/000113668.
Zhu, Yanfang, Qitian Wang, Jin Hu, Liwei Zhu, Jiancheng Wang, Shuijin Zhu, and Yajing Guan. 2013. “High Resolution Melting Curve Analysis?: An Efficient Method for Fingerprinting of Hybrid Rice Cultivars and Their Parental Lines.” Australian Journal of Crop Science 7 (13): 2048–53.
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