Vol. 2025 No. 2 (2025)
Articles

The application of methylation-sensitive amplified polymorphism (MSAP)in ecology

Hyun-jun Park
The Korea Science and Technology Center, The First Building, Room 62022, Teheran-ro 7-gil, Gangnam-gu Seoul 06130, Republic of Korea
Ji-hoon Son
The Korea Science and Technology Center, The First Building, Room 62022, Teheran-ro 7-gil, Gangnam-gu Seoul 06130, Republic of Korea

Published 17-03-2025

Keywords

  • Methylation-Sensitive Amplified Polymorphism (MSAP),
  • Ecology,
  • Population Variation,
  • Ecological Epigenetics

How to Cite

[1]
H.- jun Park and J.- hoon Son, “The application of methylation-sensitive amplified polymorphism (MSAP)in ecology”, Camb. Sci. Adv., vol. 2025, no. 2, pp. 25–31, Mar. 2025, doi: 10.62852/csa/2025/136.

Abstract

DNA methylation is one of the most important epigenetic modifications in living organisms and its application in ecology is becoming increasingly widespread. Based on the collection and review of relevant literature in ecological epigenetics, this paper introduces the principles, advantages, and limitations of Methylation-Sensitive Amplified Polymorphism (MSAP) technology, as well as its applications and prospects in ecology. MSAP has become a powerful tool for studying DNA methylation levels due to its wide application and ease of operation. It is particularly useful in exploring how organisms rapidly adapt to habitat changes and how invasive species overcome genetic bottlenecks. MSAP technology can effectively reveal epigenetic differences within or between biological populations, serving as a valuable complement to the study of genetic diversity and genetic variation.

References

  1. Hong, L., &Deng, X.X., 2005.DNA methylation analysis of navel orange varieties using MSAP technology. Scientia Agricultura Sinica,38(11):2301-2307.
  2. Angers B, Castonguay E and Massicotte R,2010. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Molecular Ecology,19(7):1283-1295.
  3. Bossdorf O, Arcuri D, Richards C L and Pigliucci M,2010. Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evolutionary Ecology,24(3):541-553
  4. Bossdorf O, Richards C L and Pigliucci M, 2008.Epigenetics for ecologists. Ecology Letters, 11(2): 106-115.
  5. Chen RJ, He L, Sun LZ, Wang HT, Song J and Liu W, 2015.Effects of copper stress on the growth and genomic DNA methylation of Arabidopsis thaliana seedlings. Chinese Journal of Ecology, 34(9):2650-2657.
  6. Chwedorzewska K J and Bednarek PT,2012. Genetic and epigenetic variation in a cosmopolitan grass Poa annua from Antarctic and Polish populations. Polish Polar Research,33 (1):63-80.
  7. Cubas P, Vincent C and Coen E, 1999.An epigenetic mutation responsible for natural variation in floral symmetry. Nature, 401:157-161.
  8. Gao L X, Geng Y P, Li B, Chen J K and Yang J,2010. Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant, Cell and Environment,33(11):1820-1827.
  9. Guarino F, Cicatelli A, Brun du G, Heinze B and Castiglione S, 2015.Epigenetic diversity of clonal white poplar (Populus alba L.) populations: could methylation support the success of vegetative reproduction strategy? P Lo S ONE,10(7): e0131480.
  10. Herrera C M and Baza ga P,2010. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytologist, 187(3):867-876.
  11. Herrera C M and Baza ga P,2011. Un tang ling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Molecular Ecology, 20(8): 1675-1688.
  12. Herrera C M, Pozo M I and Baza ga P,2012. Jack of all nectars, master of most: DNA methylation and the epigeneticbasis of niche width in a flower-living yeast. Molecular Ecology, 21(11): 2602-2616.
  13. Jablonka E and Lamb M J,2006. The evolution of information in the major transitions. Journal of Theoretical Biology,239 (2):236-246.
  14. Jablonka E and Raz G,2009. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. The Quarterly Review of Biology,84(2):131-176.
  15. Johannes F, Porcher E, Teixeira F K, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F and Colot V,2009. Assessing the impact of transgenerational epigenetic variation on complex traits. P Lo S Genetics,5(6): e1000530.
  16. Kucharski R, Maleszka J, Foret S and Maleszka R,2008. Nutritional control of reproductive status in honeybees via DNA methylation. Science,319:1827-1830.
  17. Liu S, Sun KP, Jiang TL, Ho JP, Liu B and Feng J,2012. Natural epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations. Molecular Genetics and Genomics, 287(8): 643-650.
  18. Manning K, Tor M, Poole M, Hong Y G, Thompson AJ, King GJ, Giovannoni J J and Seymour GB,2006. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genetics,38(8):948-952.
  19. Martin L B, Liebl A L, Trotter J H, Richards C L, McCoy K and McCoy MW, 2011. Integrator networks: illuminating the black box linking genotype and phenotype. Integrative and Comparative Biology,51(4):514-527.
  20. Massicotte R and Angers B, 2012. General-purpose genotype or how epigenetics extend the flexibility of a genotype. Genetics Research International, ID 317175.
  21. Massicotte R, Whitelaw E and Angers B,2011. DNA methylation: a source of random variation in natural populations. Epigenetics ,6(4):421-427.
  22. Mc Clell and M, Nelson M and Raschke E,1994. Effect of sitespecific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Research,22 (17):3640-3659.
  23. Morgan H D, Sutherland H G E, Martin D I K and Whitelaw E, 1999.Epigenetic inheritance at the agouti locus in the mouse. Nature Genetics,23(3):314-318.
  24. Pigliucci M, 2010.Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor. Philosophical Transactions of the Royal Society B: Biological Sciences, 365: 557-566.
  25. Platt A, Gugger P F, Pellegrini M and Sork V L,2015. Genome wide signature of local adaptation linked to variable CpG methylation in oak populations. Molecular Ecology, 24 (15): 3823-3830.
  26. Rak Yan VK, Chong S, Champ M E, Cuthbert P C, Morgan H D, Luu K V K and Whitelaw E,2003. Transgenerational inheritance of epigenetic states at the murine Axin Fu allele occurs after maternal and paternal transmission. Procedings of the National Academy of Sciences of the United States of America,100(5):2538-2543.
  27. Reyna-López E G, Simpson J and Ruiz-Herrera J,1997. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Molecular and General Genetics,253(6):703-710.
  28. Richards C L, Bossdorf O and Verhoeven K J F,2010. Understanding natural epigenetic variation. New Phytologist,187 (3):562-564.
  29. Richards C L, Hanzawa Y, Katari M S, Ehrenreich I M, Engelmann K E and Purugganan M D,2009. Perspectives on ecological and evolutionary systems biology//Coruzzi G M and Gutierrez R A. Annual Plant Reviews Volume 35: Plant Systems Biology. Oxford, UK: Wiley-Blackwell: 331-349.
  30. Richards C L, Rosas U, Banta J, Bhambhra N and Purugganan MD, 2012a.Genome-wide patterns of Arabidopsis gene expression in nature. P Lo S Genetics,8(4): e1002662.
  31. Richards C L, Schrey A W and Pigliucci M, 2012b.Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecology Letters, 15(9): 1016- 1025.
  32. Richards C L, Walls R L, Bailey J P, Parameswaran R, George T and Pigliucci M, 2008. Plasticity in salt tolerance traits allows or invasion of novel habitat by Japanese knotweed s. I. (Fallopia japonica and F.×bohemica, Polygonaceae). American Journal of Botany, 95(8): 931-942.
  33. Richards E J,2006. In herited epigenetic variation—revisiting soft in heritance. Nature Reviews Genetics,7(5):395-401.
  34. Roberts R J, Vincze T, Posfai J and Macelis D,2007. RE BASE—enzymes and genes for DNA restriction and modification. Nucleic Acids Research,35: D269-D270.
  35. Robertson M and Richards C,2015. Opportunities and challenges of next-generation sequencing applications in ecological epigenetics. Molecular Ecology, 24(15): 3799- 3801.
  36. Roy N, Choi J Y, Lim M J, Lee S I, Choi H J and Kim N S, 2015.Genetic and epigenetic diversity among dent, waxy, and sweet corns. Genes &Genomics,37(10):865-874.
  37. Salmon A, Ainouche M L and Wendel J F, 2005.Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology, 14(4): 1163-1175.
  38. Salmon A, Clotault J, Jenczewski E, Chable V and Manzanares-Dauleux M J, 2008.Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Science,174 (1):61-70.
  39. Schrey A W, Alvarez M, Foust C M, Kilvitis H J, Lee J D, Liebl A L, Martin L B, Richards C L and Robertson M, 2013.Ecological epigenetics: beyond MS-AFLP. Integrative and Comparative Biology,53(2):340-350.
  40. Schrey A W, Coon C A C, Grispo M T, Awad M, Imboma T, McCoy E D, Mushinsky HR, Richards C L and Martin L B, 2012.Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genetics Research International, ID 979751.
  41. Verhoeven K J F, Jansen J J, van Dijk PJ and Biere A,2010. Stress-induced DNA methylation changes and their heritability in asexual dandelions. New Phytologist,185(4):1108-1118.
  42. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M and Zabeau M,1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research,23(21):4407-4414.
  43. Xin C H, Hou R K, Wu F, Zhao Y B, Xiao H H, Si W T, Ali ME, Cai L and Guo J B,2015. Analysis of cytosine methylation status in potato by methylation-sensitive amplified polymorphisms under low-temperature stress. Journal of Plant Bi- ology,58(6):383-390.
  44. Zeng F S, Li L L, Liang N S, Wang X, Li X and Zhan Y G, 2015.Salt tolerance and alterations in cytosine methylation in the interspecific hybrids of Fraxinus elutina and Fraxinus mandshurica. Euphytica, 205(3):721-737.