Molecular studies of coralberry (Ardisia crenata Sims; Primulaceae) from Thailand based on SCoT markers

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SUPARMAN SUPARMAN
PIMWADEE PORNPONGRUNGRUENG
PRANOM CHANTARANOTHAI

Abstract

Abstract. Suparman S, Pornpongrungrueng P, Chantaranothai P. 2023. Molecular studies of coralberry (Ardisia crenata Sims; Primulaceae) from Thailand based on SCoT markers. Biodiversitas 24: 3183-3189. A coralberry (Ardisia crenataSims) is the most common species of Ardisia Sw. distributed widely in Thailand. The grouping of the species for intraspecific based on morphometric characters was unstable. Some molecular primers were used by researchers to separate species. In this molecular study, six selected SCoT of 36 primers, i.e., primers no. 13, 14, 15, 19, 20, and 21, displayed high polymorphic and resolving power in A. crenata from 14 different natural populations in Thailand. This marker separated all taxa into two groups from different floristic regions. In contrast, this result did not support the classification of the intraspecific level of A. crenata based on continued morphological characteristics. For the conclusion that this study was recorded as the first one using the SCoT marker on the Ardisiaand the primer worked well in A. crenata and was recommended for other species in Ardisia.

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References
Abdel-Mawgood, A. 2012. DNA based techniques for studying genetic diversity. In M. Caliskan (eds), Genetic Diversity in Microorganisms (pp. 95–122). IntechOpen. https://doi.org/10.5772/33509
Abuzayed, M., El-Dabba, N., Frary, A., Doganlar, S. 2017. GDdom: an online tool for calculation of dominant marker gene diversity. Biochemical Genetics, 55(2), 155–157. https://doi.org/10.1007/s10528-016-9779-0
Amiryousefi, A., Hyvönen, J., Poczai, P. 2018. iMEC: Online Marker Efficiency Calculator. Applications in Plant Sciences, 6(6), 4–7. https://doi.org/10.1002/aps3.1159
Arif, I. A., Bakir, M. A., Khan, H. A., Al Farhan, A. H., Al Homaidan, A. A., Bahkali, A. H., Al Sadoon, M., Shobrak, M. 2010. A brief review of molecular techniques to assess plant diversity. International Journal of Molecular Sciences, 11(5), 2079–2096. https://doi.org/10.3390/ijms11052079
Bhattacharyya, P., Van Staden, J. 2018. Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa. Physiology and Molecular Biology of Plants, 24(4), 631–641. https://doi.org/10.1007/s12298-018-0523-6
Bi?kowski, J., Miks, S. 2018. Gene-Calc [Computer software]. Www.Gene- Calc.Pl.
Chen, X., Li, N., Shen, L. 2001. The mating system of Ardisia crenata var. bicolor (Myrsinaceae), a subtropical understory shrub, in Tiantong National Forest Park, Zhejiang Province. Acta Phytoecologica Sinica, 25(2), 161–165.
Chesnokov, Y. V., Artemyeva, A. M. 2015. Evaluation of the measure of polymorphism information of genetic diversity. Agricultural Biology, 50(5), 571–578. https://doi.org/10.15389/agrobiology.2015.5.571rus
Collard, B. C. Y., Mackill, D. J. 2009. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 27, 86–93. https://doi.org/10.1007/s11105-008-0060-5
Cota-Sánchez, J. H., Remarchuk, K., & Ubayasena, K. 2006. Ready to use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue. Plant Molecular Biology Reporter, 24(2), 161–167. https://doi.org/10.1007/BF02914055
De Riek, J., Calsyn, E., Everaert, I., Van Bockstaele, E., De Loose, M. 2001. AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theor Appl Genet, 103, 1254 – 1265.
Doyle, J. J., Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. In Phytochemical Bulletin (Vol. 19, Issue 1, pp. 11–15). https://webpages.uncc.edu/~jweller2/pages/BINF8350f2011/BINF8350_Readings/Doyle_plantDNAextractCTAB_1987.pdf
Etminan, A., Pour-Aboughadareh, A., Mohammadi, R., Ahmadi-Rad, A., Noori, A., Mahdavian, Z., Moradi, Z. 2016. Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnology and Biotechnological Equipment, 30(6), 1075–1081. https://doi.org/10.1080/13102818.2016.1228478
Gorji, A. M., Poczai, P., Polgar, Z., Taller, J. 2011. Efficiency of arbitrarily amplified dominant markers (SCOT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid Potato. American Journal of Potato Research, 88(3), 226–237. https://doi.org/10.1007/s12230-011-9187-2
Guo, D. L., Zhang, J. Y., Liu, C. H. 2012. Genetic diversity in some grape varieties revealed by SCoT analyses. Molecular Biology Reports, 39, 5307–5313. https://doi.org/10.1007/s11033-011-1329-6
Hammer, O., Harper, D. A. T., Ryan, P. D. 2001. PAST: paleontological statistic software package for education and data analysis. Palaeontologia Electronica.
Hu, C. M., Vidal, J. E. 2004. Myrsinaceae. In P. Morat (Ed.), Flore du Cambodge du Laos et du Vietnam. Museum National D;historie Naturelle.
Jeffreys, A. J. 2013. The man behind the DNA fingerprints: An interview with Professor Sir Alec Jeffreys. Investigative Genetics, 4(21), 1–7. https://doi.org/10.1186/2041-2223-4-21
Larsen, K., Hu, C. 1996. Myrsinaceae. In T. Smitinand & K. Larsen (eds), Flora of Thailand (Vol. 6, Issue 2).
Lee, A. K., Suh, J. K., Roh, M. S., Slovin, J. P. 2003. Analysis of genetic relationships of Ardisia spp. using RAPD markers. Journal of Horticultural Science and Biotechnology, 78(1), 24–28. https://doi.org/10.1080/14620316.2003.11511580
Mahjbi, A., Baraket, G., Oueslati, A., Salhi-Hannachi, A. 2015. Start Codon Targeted (SCoT) markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species. Biochemical Systematics and Ecology, 61, 390–398. https://doi.org/10.1016/j.bse.2015.07.017
McDermott, J. M., McDonald, B. A. 1993. Gene flow in plant pathosystems. Annual Review of Phytopathology, 31, 353–373. https://doi.org/10.1146/annurev.py.31.090193.002033
Mu, H. P., Hong, L., Cao, H. L., Wang, Z. F., Li, Z. C., Shen, H., Wang, Z. M., Ye, W. H. 2010. Genetic variation of ardisia crenata in south china revealed by nuclear microsatellite. Journal of Systematics and Evolution, 48(4), 279–285. https://doi.org/10.1111/j.1759-6831.2010.00081.x
Robinson, J. P., Harris, S. A. 2000. Amplified fragment length polymorphisms and microsatellites: A phylogenetic perspective. In E. Gillett (eds) In Which DNA Marker for Which Purpose? Hamburg: Institut fur Forestgenetik und Forestpflanzenzuchtung, pp.95-121
Satya, P., Karan, M., Jana, S., Mitra, S., Sharma, A., Karmakar, P. G., Ray, D. P. 2015. Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta Gene, 3, 62–70. https://doi.org/10.1016/j.mgene.2015.01.003
Sims, J. (1818). Ardisia crenata. Dwarf Ardisia. Curtis’s botanical magazine, 45, Pl 1950. London.
Smitinand, T. 1958. The genus Dipterocarpus Gaertn. Thai Forest Bulletin (Botany), 4, 1–64.
Sookcharoen, S. 2020. Taxonomic status of the genus Lagere (Asteraceae) in Thailand. [Thesis]. Khon Kaen University.
The Plant List. 2020. The Plant List. The Plant List Version 1.1. Published on the Internet; http://www.theplantlist.org/ (accessed 20st November 2020).
Vanijajiva, O. 2020. Start codon targeted (SCoT) polymorphism reveals genetic diversity of manilkara in Thailand. Biodiversitas, 21(2), 666–673. https://doi.org/10.13057/biodiv/d210232
Yang, W., Kang, X., Yang, Q., Lin, Y., Fang, M. 2013. Review on the development of genotyping methods for assessing farm animal diversity. Journal of Animal Science and Biotechnology, 4(1), 2–7. https://doi.org/10.1186/2049-1891-4-2
Yeh, F., Yang, R. C., Boyle, T., Ye, Z., & Xiyan, J. M. 1999. Microsoft Windows-based freeware for populations genetic analysis. In: molecular biology and biotechnology centre . University of Alberta.
Zhang, J., Zhao, X., Xie, W., Wang, Y. 2015. Potential of start codon targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions. Molecules, 20(4), 5987–6001. https://doi.org/10.3390/molecules20045987

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