Journals / Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi / 2026 / Issue: 1

Investigation of the Effect of Indole Acetic Acid Concentrations on Retrotransposon Movement in Oryza sativa L.

Yunus Emre Arvas(VAN YÜZÜNCÜ YIL ÜNİVERSİTESİ)0000-0001-6622-5083
Pages
—
Publication Date
2026-03-16
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

Pertinently, these study findings provide preliminary insights into the regulatory effects of IAA on mobile genetic elements.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:This study aims to investigate the effects of different Indole Acetic Acid (IAA) concentrations (0.25, 0.50, and 1 mM) on retrotransposon movement in the Kiziltan rice variety.
📊
Key Findings & Data:This study chooses rice as it is a strategic agricultural product that serves as the primary food source for people worldwide.
💡
Conclusion & Impact:Pertinently, these study findings provide preliminary insights into the regulatory effects of IAA on mobile genetic elements.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:IAA · Retrotransposon · IRAP

Abstract

This study aims to investigate the effects of different Indole Acetic Acid (IAA) concentrations (0.25, 0.50, and 1 mM) on retrotransposon movement in the Kiziltan rice variety. This study chooses rice as it is a strategic agricultural product that serves as the primary food source for people worldwide. Analysis of the effects of the growth regulator hormone IAA at different concentrations on rice plants is of great importance for understanding hormonal regulation of plant development and for developing applications to increase yield. Our results reveal the relationships among genetic mobility, plant development, and hormone levels, with variable IAA concentrations regulating plant developmental processes and promoting root and shoot growth of rice. At specific doses, this study found that IAA application enhanced the O. sativa cv. Kiziltan rice yield. The rice grown under different IAA concentrations for 15 days showed distinct band profiles and polymorphisms. The Jaccard similarity index calculations revealed polymorphism rates ranged from 62% to 100% for Hopi, 0% to 100% for Houba, 53% to 100% for Osr30, and 62% to 100% for Sukkula in IRAP analyses. Pertinently, these study findings provide preliminary insights into the regulatory effects of IAA on mobile genetic elements.

🔖

Cite This Article

Arvas, Y. E. (2026). Investigation of the Effect of Indole Acetic Acid Concentrations on Retrotransposon Movement in Oryza sativa L.. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, Issue: 1. https://doi.org/10.29133/yyutbd.1709768

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (50)

  1. Akakpo, R., Carpentier, M. c., Hsing, Y. I., & Panaud, O. (2020). The impact of transposable elements on the structure, evolution and function of the rice genome. New Phytologist.
  2. Ali, S., Khan, N., & Tang, Y. (2022). Epigenetic marks for mitigating abiotic stresses in plants. Journal of Plant Physiology, 275, 153740.
  3. Arvas, Y. E. (2026). LC-MS/MS-based phenolic profiling and IRAP-PCR analysis reveal biochemical and genomic responses of flax (Linum usitatissimum L.) to salt stress. Molecular Biology Reports, 53(1), 218.
  4. Arvas, Y. E., Kocaçalışkan, İ., Ordu, E., & Erişen, S. (2022a). Comparative retrotransposon analysis of mutant and non-mutant rice varieties grown at different salt concentrations. Biotechnology & Biotechnological Equipment, 36(1), 25-34.
  5. Arvas, Y. E., Yolci, M. S., & Marakli, S. (2022b). Investigation the effect of drought stress on tolerant and resistant rice (Oryza sativa L.) varieties in terms of morphologic and genetic characters. Genetic Resources and Crop Evolution, 70(2), 427-436. https://doi.org/10.1007/s10722-022-01436-0
  6. Ashapkin, V. V., Kutueva, L. I., Aleksandrushkina, N. I., & Vanyushin, B. F. (2019). Epigenetic regulation of plant gametophyte development. International Journal of Molecular Sciences, 20(12), 3051.
  7. Cakmak, B., Marakli, S., & Gozukirmizi, N. (2017). Sukkula retrotransposon movements in the human genome. Biotechnology & Biotechnological Equipment, 31(4), 756-760.
  8. Cavrak, V. V., Lettner, N., Jamge, S., Kosarewicz, A., Bayer, L. M., & Mittelsten Scheid, O. (2014). How a retrotransposon exploits the plant's heat stress response for its activation. PLoS genetics, 10(1), e1004115.
  9. Chen, H., Chen, M., Yang, S., Zhou, H., Xie, Z., Huang, Y., & Chen, D. (2025). Genomic and translational insights into eIF2B-mediated salt tolerance in sea rice HD961. BMC biology, 23(1), 333.
  10. EL Sabagh, A., Islam, M. S., Hossain, A., Iqbal, M. A., Mubeen, M., Waleed, M., Reginato, M., Battaglia, M., Ahmed, S., & Rehman, A. (2022). Phytohormones as growth regulators during abiotic stress tolerance in plants. Frontiers in Agronomy, 4, 765068.
  11. Feng, Y., Tian, B., Xiong, J., Lin, G., Cheng, L., Zhang, T., Lin, B., Ke, Z., & Li, X. (2024). Exploring IAA biosynthesis and plant growth promotion mechanism for tomato root endophytes with incomplete IAA synthesis pathways. Chemical and Biological Technologies in Agriculture, 11(1), 187.
  12. Fornasiero, A., Feng, T., Al-Bader, N., Alsantely, A., Mussurova, S., Hoang, N. V., Misra, G., Zhou, Y., Fabbian, L., & Mohammed, N. (2025). Oryza genome evolution through a tetraploid lens. Nature Genetics, 57(5), 1287-1297.
  13. Fort, V., Khelifi, G., & Hussein, S. M. (2021). Long non-coding RNAs and transposable elements: A functional relationship. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1868(1), 118837.
  14. Grandbastien, M.-A., Audeon, C., Bonnivard, E., Casacuberta, J., Chalhoub, B., Costa, A.-P., Le, Q. H., Melayah, D., Petit, M., & Poncet, C. (2005). Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenetic and genome research, 110(1-4), 229-241.
  15. Hassan, A. H., Mokhtar, M. M., & El Allali, A. (2024). Transposable elements: multifunctional players in the plant genome. Frontiers in plant science, 14, 1330127.
  16. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H., & Kanda, M. (1996). Retrotransposons of rice involved in mutations induced by tissue culture. Proceedings of the National Academy of Sciences, 93(15), 7783-7788.
  17. Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., & Paszkowski, J. (2011). An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature, 472(7341), 115-119.
  18. Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles, 44, 223-270.
  19. Kaeppler, S. M., Kaeppler, H. F., & Rhee, Y. (2000). Epigenetic aspects of somaclonal variation in plants. Plant Molecular Biology, 43(2), 179-188.
  20. Kartal-Alacam, G., Yilmaz, S., Marakli, S., & Gozukirmizi, N. (2014). Sukkula retrotransposon insertion polymorphisms in barley. Russian Journal of Plant Physiology, 61(6), 828-833.
  21. Kidwell, K. K., & Osborn, T. C. (1992). Simple plant DNA isolation procedures. In Plant genomes: methods for genetic and physical mapping (pp. 1-13). Springer.
  22. Li, J., & Jiong, F. (2024). Genomic diversity and evolutionary mechanisms in the Oryza genus: a comparative analysis. Genomics and Applied Biology, 15.
  23. Lisch, D. (2009). Epigenetic regulation of transposable elements in plants. Annual review of plant biology, 60, 43-66.
  24. Makarevitch, I., Waters, A. J., West, P. T., Stitzer, M., Hirsch, C. N., Ross-Ibarra, J., & Springer, N. M. (2015). Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS genetics, 11(1), e1004915.
  25. Maraklı, S. (2018). Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. Marmara Fen Bilimleri Dergisi, 30(3), 299-304.
  26. Marzi, D., Brunetti, P., Saini, S. S., Yadav, G., Puglia, G. D., & Dello Ioio, R. (2024). Role of transcriptional regulation in auxin-mediated response to abiotic stresses. Frontiers in Genetics, 15, 1394091.
  27. Naito, K., Zhang, F., Tsukiyama, T., Saito, H., Hancock, C. N., Richardson, A. O., Okumoto, Y., Tanisaka, T., & Wessler, S. R. (2009). Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature, 461(7267), 1130-1134.
  28. Noormohammadi, Z., Torabizadeh, E., Farahani, F., Alishah, O., & Sheidai, M. (2020). Genetic and physiological analysis of cotton cultivars under salt stress. Genetika, 52(2), 751-764.
  29. Paul, M., Thriveni, V., Kumar, P., Alapati, R., Ashoka, P., Sampath, V., & Nambiar, R. (2025). Transposable Elements in Plant Genomics: Drivers of Evolution, Adaptation, and Crop Improvement. Journal of Advances in Biology & Biotechnology, 28(4), 435-447.
  30. Pecinka, A., Dinh, H. Q., Baubec, T., Rosa, M., Lettner, N., & Scheid, O. M. (2010). Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. The Plant Cell, 22(9), 3118-3129.
  31. Perrella, G., Bäurle, I., & van Zanten, M. (2022). Epigenetic regulation of thermomorphogenesis and heat stress tolerance. New Phytologist, 234(4), 1144-1160.
  32. Raheem, A., Shaposhnikov, A., Belimov, A. A., Dodd, I. C., & Ali, B. (2018). Auxin production by rhizobacteria was associated with improved yield of wheat (Triticum aestivum L.) under drought stress. Archives of Agronomy and Soil Science, 64(4), 574-587.
  33. Ramakrishnan, M., Satish, L., Kalendar, R., Narayanan, M., Kandasamy, S., Sharma, A., Emamverdian, A., Wei, Q., & Zhou, M. (2021). The dynamism of transposon methylation for plant development and stress adaptation. International Journal of Molecular Sciences, 22(21), 11387.
  34. Ranjan, A., Rajput, V. D., Prazdnova, E. V., Gurnani, M., Sharma, S., Bhardwaj, P., Shende, S. S., Mandzhieva, S. S., Sushkova, S., & Minkina, T. (2024). Augmenting abiotic stress tolerance and root architecture: The function of phytohormone-producing PGPR and their interaction with nanoparticles. South African Journal of Botany, 167, 612-629.
  35. Sharma, P., Sharma, C. L., Rana, V. S., & Sharma, S. (2025). Plant Growth Regulators–Structure, Biosynthesis, and Mode of Action. In Advances in Growth Regulation of Fruit Crops (pp. 52-65). CRC Press.
  36. Shirasu, K., Schulman, A. H., Lahaye, T., & Schulze-Lefert, P. (2000). A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome research, 10(7), 908-915.
  37. Temel, A., Kartal, G., & Gozukirmizi, N. (2008). Genetic and epigenetic variations in barley calli cultures. Biotechnology & Biotechnological Equipment, 22(4), 911-914.
  38. Tossolini, I., Mencia, R., Arce, A. L., & Manavella, P. A. (2025). The genome awakens: transposon-mediated gene regulation. Trends in plant science.
  39. Tufan, A. F., Ibisoglu, M. S., Yilmaz, S., & Gozukirmizi, N. (2020). Investigation of rice (Oryza sativa L.) retrotransposons in different taxa. Genetic Resources and Crop Evolution, 1-7.
  40. Turkoglu, A. (2023). Effects of mammalian sex hormones on regeneration capacity, retrotransposon polymorphism and genomic instability in wheat (Triticum aestivum L.). Plant Cell, Tissue and Organ Culture (PCTOC), 152(3), 647-659.
  41. Verma, S., & Verma, P. K. (2025). Mobile Genetic Elements and Abiotic Stress Tolerance. In Decoding Non-Coding RNA: Enhancing Plant Abiotic Stress Tolerance (pp. 125-140). Springer.
  42. Vicient, C. M., Jaaskelainen, M. J., Kalendar, R., & Schulman, A. H. (2001). Active retrotransposons are a common feature of grass genomes. Plant physiology, 125(3), 1283-1292.
  43. Vuorinen, A. L., Kalendar, R., Fahima, T., Korpelainen, H., Nevo, E., & Schulman, A. H. (2018). Retrotransposon-based genetic diversity assessment in wild emmer wheat (Triticum turgidum ssp. dicoccoides). Agronomy, 8(7), 107.
  44. Wang, R., & Estelle, M. (2014). Diversity and specificity: auxin perception and signaling through the TIR1/AFB pathway. Current opinion in plant biology, 21, 51-58.
  45. Wójcikowska, B. (2025). Involvement of nitrilases in auxin biosynthesis and their role in plant development and stress response. Plant and Cell Physiology, pcaf152.
  46. Yasuda, K., Ito, M., Sugita, T., Tsukiyama, T., Saito, H., Naito, K., Teraishi, M., Tanisaka, T., & Okumoto, Y. (2013). Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Molecular Breeding, 32(3), 505-516.
  47. Yetgin, Ö. (2019). Retrotransposon analysis in rice and Turkish upland rice growth under boron stress Ondokuz Mayis University]. Samsun-Turkey.
  48. Yokosho, K., Yamaji, N., Fujii-Kashino, M., & Ma, J. F. (2016). Retrotransposon-mediated aluminum tolerance through enhanced expression of the citrate transporter OsFRDL4. Plant physiology, 172(4), 2327-2336.
  49. Yu, Y., Xu, X., Hu, Y., Ding, Y., & Chen, L. (2024). Indole-3-acetic acid (IAA) and sugar mediate endosperm development in rice (Oryza sativa L.). Rice, 17(1), 66.
  50. Yuzbasioglu, G., Yilmaz, S., Marakli, S., & Gozukirmizi, N. (2016). Analysis of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice. Biotechnology & Biotechnological Equipment, 30(2), 213-218.