Development of SSR markers and assessment of genetic diversity in native Nepenthes spp. in southern Thailand
DOI:
https://doi.org/10.1590/2447-536X.v31.e312847Keywords:
carnivorous plants, genetic identification, Nepenthes spp., pitcher plant, simple sequence repeatsAbstract
Nepenthes spp. (Nepenthaceae) is one of the popular genera of carnivorous plants, which has a special leaf modification with varying shapes, sizes, and shades of color. These plants exhibit high variation within species and populations, making it difficult to classify them by morphology. As a result, molecular techniques are needed to identify genetic diversity. Therefore, this study aimed to generate simple sequence repeat (SSR) markers and assess the genetic diversity of nine native Nepenthes spp. in southern Thailand. In the present study, a total of 20 SSR primer pairs containing dinucleotide or trinucleotide motifs were identified from 2,138 nucleotides and 41 ESTs of Nepenthaceae, and 950 nucleotides of carnivorous plants from that database were retrieved from GenBank. Only 10 were polymorphic, showing 2–7 alleles and, on average, 3.7 alleles per locus. Based on SSR markers, the nine Nepenthes spp. were clustered into two main groups by SSR scoring data using UPGMA cluster analysis, with a cophenetic correlation of 0.76. This is the first report that identified N. mirabilis var. globosa as distinct from N. mirabilis by SSR markers. The results suggested that SSR markers can successfully reveal variability among Nepenthes spp. They can be useful to evaluate genetic diversity studies, provide practical information for parental selection, assist breeding programs, and the result is important to the conservation action of endangered species.
Downloads
References
ANUNIWAT, A.; CHAVEERACH, A.; TANEE, T.; SUDMOON, R. Development of SCAR markers for species identification of the genus Nepenthes (Nepenthaceae). Pakistan Journal of Biological Sciences, v. 12, n. 22, p. 1455–1461, 2009. https://doi.org/10.3923/pjbs.2009.1455.1461
BIANCHI, A.; LEE, C. C.; GOLOS, M. R.; MEY, F. S.; MANSUR, M.; MAMBRASAR, Y. M.; ROBINSON, A. S. Nepenthes diabolica (Nepenthaceae), a new species of toothed pitcher plant from Central Sulawesi. Phytotaxa, v. 464, n. 1, p. 29–48, 2020. https://doi.org/10.11646/phytotaxa.464.1.2
BLISCHAK, P. D.; KUBATKO, L. S.; WOLFE, A. D. SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. Bioinformatics, v. 34, n. 3, p. 407–415, 2018. https://doi.org/10.1093/bioinformatics/btx587
BREARLEY, F. Q. Nutrient and metal concentrations in Nepenthes macfarlanei Hemsl. (Nepenthaceae) from a Malaysian montane forest. Notulae Scientia Biologicae, v. 13, n. 2, p. 10976, 2021. https://doi.org/10.15835/nsb13210976
CATALANO, M. Nepenthes suratensis M. Catal. sp. nov. In: CATALANO, M. Nepenthes della Thailandia: Diario di viaggio. Prague: WOW s.r.o., 2010b. p. 36.
CATALANO, M. Nepenthes andamana M. Catal. sp. nov. In: CATALANO, M. Nepenthes della Thailandia: Diario di viaggio. Prague: WOW s.r.o., 2010c. p. 34.
CATALANO, M. Nepenthes mirabilis var. globosa M. Catal. var. nov. In: CATALANO, M. Nepenthes della Thailandia: Diario di viaggio. Prague: WOW s.r.o., 2010a. p. 40.
CHAVEERACH, A.; TANOMTONG, A.; SUDMOON, R.; TANEE, T. Genetic diversity among geographically separated populations of Nepenthes mirabilis. Biologia, v. 61, n. 3, p. 295–298, 2006. https://doi.org/10.2478/s11756-006-0054-4
CHEEK, M. R.; JEBB, M. H. P.; MURPHY, B. A. A classification of functional pitcher types in Nepenthes (Nepenthaceae). Planta Carnivora, v. 40, n. 2, p. 22–43, 2020. https://doi.org/10.1101/852137
CROSS, A. T.; KRUEGER, T. A.; GONELLA, P. M.; ROBINSON, A. S.; FLEISCHMANN, A. S. Conservation of carnivorous plants in the age of extinction. Global Ecology and Conservation, v. 24, e01272, 2020. https://doi.org/10.1016/j.gecco.2020.e01272
CROSS, A. T.; VAN DER ENT, A.; WICKMANN, M.; SKATES, L. M.; SUMAIL, S.; GEBAUER, G.; ROBINSON, A. S. Capture of mammal excreta by Nepenthes is an effective heterotrophic nutrition strategy. Annals of Botany, v. 130, n. 7, p. 927–938, 2022. https://doi.org/10.1093/aob/mcac134
DANČÁK, M.; MAJESKÝ, Ľ.; ČERMÁK, V.; GOLOS, M. R.; PŁACHNO, B. J.; TJIASMANTO, W. First record of functional underground traps in a pitcher plant: Nepenthes pudica (Nepenthaceae), a new species from North Kalimantan, Borneo. PhytoKeys, v. 201, p. 77–97, 2022. https://doi.org/10.3897/phytokeys.201.82872
DOYLE, J. J.; DOYLE, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, v. 19, p. 11–15, 1987.
GHAZALLI, M. N.; TAMIZI, A. A.; NIKONG, D.; BESI, E. E.; MAT ESA, M. I.; NORDIN, A. R. M.; LATIFF, A.; ZAINI, A. Z.; SHAKRI, M. A. Nepenthes latiffiana and N. domei (Nepenthaceae), two new species of pitcher plants from Terengganu, Peninsular Malaysia. Webbia, v. 75, n. 1, p. 5–28, 2020. https://doi.org/10.36253/jopt-7950
GHAZALLI, M. N.; TAMIZI, A. A.; NIKONG, D.; MAT ESA, M. I.; BESI, E. E.; SALLEH, S.; TALIP, N.; LATIFF, A. Comparative leaf anatomy of ten Nepenthes L. species (Nepenthaceae) from Peninsular Malaysia. Notulae Scientia Biologicae, v. 13, n. 4, 10980, 2021. https://doi.org/10.15835/nsb13410980
HAMM, T. P.; NOWICKI, M.; BOGGESS, S. L.; RANNEY, T. G.; TRIGIANO, R. N. A set of SSR markers to characterize genetic diversity in all Viburnum species. Scientific Reports, v. 13, 5343, 2023. https://doi.org/10.1038/s41598-023-31878-0
HU, L.; WANG, J.; WANG, X.; ZHANG, D.; SUN, Y.; LU, T.; SHI, W. Development of SSR markers and evaluation of genetic diversity of endangered plant Saussurea involucrata. Biomolecules, v. 14, n. 8, p. 1010, 2024. https://doi.org/10.3390/biom14081010
HUSSAIN, H.; NISAR, M. Assessment of plant genetic variations using molecular markers: a review. Journal of Applied Biology and Biotechnology, v. 8, p. 99–109, 2020. https://doi.org/10.7324/JABB.2020.80514
MANJU, Y.; KUMAR, Y. Y.; PUSHPENDRA, K.; KUMAR, S. R.; RENU, Y.; PAWAN, K.; SHAILY, J.; MAHESH, R.; NEELAM, Y.; UPADHYAYA, H. D.; RAJENDRA, K. Molecular diversity analysis as an improvement tool for pigeonpea [Cajanus cajan (L.)]. Research Journal of Biotechnology, v. 12, n. 9, p. 75–86, 2017. http://oar.icrisat.org/id/eprint/10340
MANSUR, M.; BREARLEY, F. Q.; ESSEEN, P. J.; RODE-MARGONO, E. J.; TARIGAN, M. R. M. Ecology of Nepenthes clipeata on Gunung Kelam, Indonesian Borneo. Plant Ecology and Diversity, v. 14, n. 3–4, p. 195–203, 2021. https://doi.org/10.1080/17550874.2021.1984602
MANSUR, M.; SALAMAH, A.; MIRMANTO, E.; BREARLEY, F. Q. Ecology of Nepenthes on Mount Talang, West Sumatra, Indonesia. Tropical Ecology, v. 65, p. 460–469, 2024. https://doi.org/10.1007/s42965-024-00333-0
MARTINS, W. S.; LUCAS, D.; CESAR, S.; NEVES, K. F. S.; BERTIOLI, D. J. WebSat – a web software for microsatellite marker development. Bioinformation, v. 3, n. 6, p. 282–283, 2009. https://doi.org/10.6026/97320630003282
MATHIANG, E. A.; SA, K. J.; PARK, H.; KIM, Y. J.; LEE, J. K. Genetic diversity and population structure of normal maize germplasm collected in South Sudan revealed by SSR markers. Plants, v. 11, n. 2787, 2022. https://doi.org/10.3390/plants11202787
MCPHERSON, S. Nepenthes – The Tropical Pitcher Plants. Vol. 1. Poole: Natural History, 2023. 739 p.
MOHN, R. A.; ZENIL-FERGUSON, R.; KRUEGER, T. A.; FLEISCHMANN, A. S.; CROSS, A. T.; YANG, Y. Dramatic difference in rate of chromosome number evolution among sundew (Drosera L., Droseraceae) lineages. Evolution, v. 77, n. 10, p. 2314–2325, 2023. https://doi.org/10.1093/evolut/qpad153
NUANLAONG, S.; MEKANAWAKUL, M.; SURANINPONG, P. Descriptions of two new species of Nepenthes (Nepenthaceae) from Thailand and their phylogenetic analysis based on AFLP technique species confirmation. Kew Bulletin, v. 77, p. 105–120, 2022. https://doi.org/10.1007/s12225-021-09997-6
OKUMUŞ, A.; DAĞIDIR, Ş. Assessment of genetic diversity on tomato (Lycopersicon esculentum) landraces using SSR molecular markers in Turkey. Frontiers in Life Sciences and Related Technologies, v. 2, n. 2, p. 51–59, 2021. https://doi.org/10.51753/flsrt.957055
OUNI, R.; ZBOROWSKA, A.; SEHIC, J.; CHOULAK, S.; HORMAZA, J. I.; GARKAVA-GUSTAVSSON, L.; MARS, M. Genetic diversity and structure of Tunisian local pear germplasm as revealed by SSR markers. Horticultural Plant Journal, v. 6, n. 2, p. 61–70, 2020. https://doi.org/10.1016/j.hpj.2020.03.003
PISTANTY, M. A. Sustainable development goals protect extinction of biodiversity Nepenthes sp: array. Pratama Medika: Jurnal Kesehatan, v. 1, n. 2, p. 69–85, 2023. https://doi.org/10.56480/pratamamedika.v1i2.833
ROHLF, F. J. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.2. New York: Exeter Software, 2000.
SAETAI, K.; KHUNPAGSEE, P.; THANANANTA, T.; THANANANTA, N. Assessment of genetic relationships and identification of Nepenthes spp. using HAT-RAPD technique. Journal of Science and Technology, v. 22, n. 2, p. 237–242, 2014.
SAUL, F.; SCHARMANN, M.; WAKATAKE, T.; RAJARAMAN, S.; MARQUES, A.; FREUND, M.; BRINGMANN, G.; CHANNON, L.; BECKER, D.; CARROLL, E.; LOW, Y. W.; LINDQVIST, C.; GILBERT, K. J.; RENNER, T.; MASUDA, S.; RICHTER, M.; VOGG, G.; SHIRASU, K.; MICHAEL, T. P.; HEDRICH, R.; ALBERT, V. A.; FUKUSHIMA, K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. Nature Plants, v. 9, p. 2000–2015, 2023. https://doi.org/10.1038/s41477-023-01562-2
SCHARMANN, M.; WISTUBA, A.; WIDMER, A. Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants. Molecular Phylogenetics and Evolution, v. 163, p. 107214, 2021. https://doi.org/10.1016/j.ympev.2021.107214
SCHWALLIER, R.; RAES, N.; DE BOER, H. J.; VOS, R. A.; VAN VUGT, R. R.; GRAVENDEEL, B. Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants. Diversity and Distributions, v. 22, n. 1, p. 97–110, 2016. https://doi.org/10.1111/ddi.12382
SHETE, G. S.; NIKAMA, S. D.; SURBHAIYYAA, S. D.; JADHAVA, M. P.; THAKARE, T. N. Analysis of genetic diversity in maize (Zea mays L.) variety using SSR markers. International Journal of Plant & Soil Science, v. 35, n. 15, p. 205–212, 2023. https://doi.org/10.9734/IJPSS/2023/v35i153098
SOLTIS, P. S.; MARCHANT, D. B.; VAN DE PEER, Y.; SOLTIS, D. E. Polyploidy and genome evolution in plants. Current Opinion in Genetics & Development, v. 35, p. 119–125, 2015. https://doi.org/10.1016/j.gde.2015.11.003
SURANINPONG, P.; NUANLAONG, S.; WUTHISUTHIMETHAVEE, S. A new classification of Thailand’s Nepenthes species by genetic analysis of AFLP markers. Acta Horticulturae, v. 1100, p. 77–82, 2015. https://doi.org/10.17660/ActaHortic.2015.1100.9
TUVESSON, S. D.; LARSSON, C. T.; ORDON, F. Use of molecular markers for doubled haploid technology: from academia to plant breeding companies. In: SEGUI-SIMARRO, J. M. (ed.) Double Haploid Technology. New York: Humana, 2021. p. 49–72. https://doi.org/10.1007/978-1-0716-1335-1_3
ZHAO, Z.; ZHANG, H.; WANG, P.; YANG, Y.; SUN, H.; LI, J.; CHEN, X.; LI, J.; JI, N.; FENG, H.; ZHAO, S. Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains. PLOS ONE, v. 18, n. 5, p. e0285754, 2023. https://doi.org/10.1371/journal.pone.0285754
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Yaowaphan Sontikun, Benjamas Somwong, Duangkhaetita Kanjanasopa, Suraphon Thitithanakul, Potjamarn Suraninpong
This work is licensed under a Creative Commons Attribution 4.0 International License.
