Oluwatoyin Ishola*1, Ugochukwu Onyemaobi 2, Bello Habibat Bolanle 3,Israel Precious Ayomide4, Glory Ojoma Simon5, Omolabake Josephine Adesona6 , Waliyat Titilayo Aremu7
1Department of Biochemistry, Kaduna State University, Kaduna, Nigeria
2Department of Biochemistry, Kaduna State University, Kaduna, Nigeria
3Department of Crop, Soil, and Pest Management, Federal University of Technology, Akure, Nigeria
4Department of Computer Science, Federal University, Lokoja, Nigeria 5
5Department of Chemical Science, Olabisi Onabanjo University, Ogun State, Nigeria6
6Department of Science Laboratory Technology, School of Scirnce and Technology, Federal Polytechnic, Ayede, Oyo State
7Department of Agricultural Economics, Ladoke Akintola University of Technology
Abstract
The study focuses on developing and validating a Python-based bioinformatics pipeline to identify genetic markers associated with curcumin biosynthesis in Curcuma longa (turmeric), addressing the challenge of variable curcumin content across turmeric varieties. Curcumin, renowned for its therapeutic properties, requires consistent levels for medicinal and commercial applications, necessitating precision breeding methods beyond traditional techniques. The study utilized genomic and phenotypic data sourced from public repositories and literature, applying next-generation sequencing technologies for data preprocessing, variant calling, association analysis, and functional annotation. Using tools such as GATK for SNP identification and PLINK for association analysis, the study revealed significant genetic markers within key genes, including MYB14 and CURS3, with regulatory SNPs linked to transcriptional control and enzymatic function. Notably, SNPs at positions 0, 3, and 18 exhibited statistically significant associations with curcumin content, highlighting their potential as markers for breeding high-curcumin turmeric varieties. The pipeline’s automation using Python enhanced efficiency and reproducibility, enabling large-scale genomic analysis. This research provides a scalable framework for genomic investigations in turmeric, contributing to targeted breeding programs aimed at optimizing curcumin production for therapeutic and commercial use.
Keywords: Curcumin, Curcuma longa, bioinformatics pipeline, genetic markers, next-generation sequencing, SNPs, transcriptional regulation, turmeric breeding, phenotypic data, functional annotation.
Preview
References
1. Aggarwal, B.B., & Harikumar, K.B. (2009). Potential therapeutic effects of curcumin, the anti-inflammatory agent, against inflammatory diseases. International Journal of Biochemistry and Cell Biology, 41(1), 40-59.
2. Aggarwal, B.B., et al. (2007). Curcumin and cancer cells: How many ways can curry kill tumor cells selectively? Biochemical Pharmacology, 76(11), 1390-1401.
3. Anand, P., et al. (2007). Bioavailability of curcumin: Problems and promises. Molecular Pharmaceutics, 4(6), 807-818.
4. Anand, P., et al. (2018). Nanomedical approaches for curcumin delivery in cancer prevention and treatment. Nanomedicine, 13(3), 77-94.
5. Atwell, S., et al. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465, 627-631.
6. Baba, K., et al. (2017). Identification of key genes and transcriptional networks associated with ginsenoside biosynthesis in Panax ginseng. Plant Molecular Biology Reporter, 35, 303-314.
7. Bansal, S.S., et al. (2019). Development and characterization of liposomal formulations of curcumin for enhanced bioavailability. Pharmaceutical Nanotechnology, 7(4), 271-280.
8. Behera, B.C., et al. (2012). Variability in curcumin content among different accessions of turmeric (Curcuma longa L.) grown in India. Indian Journal of Traditional Knowledge, 11(2), 262-266.
9. Cingolani, P., et al. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6(2), 80-92.
10. Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., … & Hoon, M. J. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422-1423.
11. Collard, B.C.Y., & Mackill, D.J. (2008). Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491), 557-572.
11. Gao, F., et al. (2016). RNAi-mediated silencing of negative regulatory genes enhances curcumin content in Curcuma longa. Plant Cell Reports, 35(9), 1905-1917.
12. Goecks, J., Nekrutenko, A., & Taylor, J. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8), R86.
12. Gaudelli, N.M., et al. (2017). Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551(7681), 464-471.
13. Goodstein, D.M., et al. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research, 40(D1), D1178-D1186.
14. Gupta, S.C., et al. (2013). Multiple targeting by curcumin as revealed by cancer cell signaling pathways in human research. Advances in Experimental Medicine and Biology, 789, 203-239.
15. Huang, X., & Han, B. (2014). Genome editing for crop improvement: Challenges and opportunities. Genomics, Proteomics & Bioinformatics, 12(6), 371-377.
16. Huang, X., et al. (2010). Genomic analysis of hybrid rice and the implications for crop improvement. Nature, 464(7291), 249-253.
17. Jinek, M., et al. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821.
18. Jurenka, J.S. (2009). Anti-inflammatory properties of curcumin: A major constituent of Curcuma longa: A review of preclinical and clinical research. Alternative Medicine Review, 14(2), 141-153.
19. Kanehisa, M., et al. (2019). KEGG: Integrating viruses and cellular organisms. Nucleic Acids Research, 47(D1), D514-D522.
20. Katsuyama, Y., et al. (2009). Functional analysis of curcumin synthase and diketide-CoA synthase in the curcuminoid biosynthetic pathway of Curcuma longa. Journal of Biological Chemistry, 284(18), 11160-11170.
21. Kumar, S., & Jain, M. (2015). The CRISPR-Cas system for plant genome editing: Advances and opportunities. Frontiers in Plant Science, 6, 170.
22. Kumar, S., et al. (2008). Expression of key enzymes and transcription factors associated with curcumin biosynthesis in Curcuma longa. Plant Physiology and Biochemistry, 46(7), 593-599.
23. Kumar, S., et al. (2016). Genetic diversity in Curcuma longa L. and its correlation with curcumin content. Journal of Medicinal Plants Research, 10(35), 621-630.
24. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754-1760.
24. Li, X., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760.
25. Lim, G.P., et al. (2001). The curry spice curcumin reduces oxidative damage and amyloid pathology in an Alzheimer transgenic mouse. Journal of Neuroscience, 21(21), 8370-8377.
26. Maiti, P., et al. (2014). Curcumin as an anti-Alzheimer’s disease agent: A review. Current Pharmaceutical Design, 20(32), 5094-5102.
27. Maheshwari, R.K., et al. (2006). Multiple biological activities of curcumin: A short review. Life Sciences, 78(18), 2081-2087.
28. Ma, Y., et al. (2019). Functional genomics and genome editing: Opportunities and challenges in medicinal plants. Frontiers in Plant Science, 10, 426.
29. Meuwissen, T.H.E., et al. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819-1829.
30. Mishra, S., et al. (2020). Sequencing and analyzing the ginger (Zingiber officinale) genome for insights into the Curcuma longa genome. Scientific Reports, 10, 11100.
31. Mohanty, S., et al. (2011). Influence of environmental factors on curcumin content in Curcuma longa L. grown across different agroclimatic regions in India. Plant Growth Regulation, 65(1), 83-91.
32. Panahi, Y., et al. (2016). Effects of curcumin on lipid profile: A meta-analysis of randomized controlled trials. Journal of Clinical Lipidology, 10(2), 356-367.
33. Panchagnula, R., et al. (2009). Mechanisms of curcumin synthesis in turmeric plants and pharmacokinetics in humans. Phytochemistry, 70(6), 656-663.
34. Paz-Ares, J., et al. (2013). The role of transcription factors in secondary metabolism. Plant Physiology, 162(4), 1204-1218.
35. Prabhakaran, M.P., et al. (2018). Collection and characterization of turmeric germplasm from across India. Journal of Medicinal Plants Research, 12(23), 401-410.
36. Purcell, S., et al. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81(3), 559-575.
37. Ravindran, P.N., et al. (2007). Genetic resources and molecular markers in turmeric: Potential applications in breeding programs. Indian Journal of Agricultural Sciences, 77(5), 255-263.
38. Sasikumar, B. (2005). Genetic diversity of Curcuma longa: Implications for breeding and curcumin enhancement. Journal of Horticultural Science and Biotechnology, 80(6), 735-739.
39. Sharma, A., et al. (2020). Genomic and transcriptomic insights into turmeric. Plant Biotechnology Journal, 18(4), 912-923.
40. Sharma, P., et al. (2012). Nutritional influences on curcumin production in Curcuma longa. Indian Journal of Agricultural Biochemistry, 25(1), 45-50.
41. Sharma, R.A., et al. (2005). Pharmacokinetics and bioavailability of curcumin in humans. Cancer Epidemiology Biomarkers & Prevention, 14(1), 69-75.
42. Shoba, G., et al. (1998). Influence of piperine on the pharmacokinetics of curcumin in animals and human volunteers. Planta Medica, 64(4), 353-356.
43. Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26(10), 1135-1145.
43. Singh, G., et al. (2013). Influence of environmental factors on turmeric (Curcuma longa) cultivation. Journal of Environmental Biology, 34(4), 999-1003.
44. Singh, R., & Tiwari, V. (2013). Organic farming practices and curcumin content in turmeric (Curcuma longa). Agricultural Research, 2(2), 161-167.
45. Stracke, R., et al. (2001). MYB transcription factors in phenylpropanoid metabolism and plant growth. Plant Cell, 13(8), 1703-1720.
46. Tetenyi, P. (2020). The global market for curcumin and turmeric products: Health benefits and trends. Nutraceuticals Journal, 15(2), 150-162.
47. Thompson, J.D., et al. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673-4680.
48. Varshney, R.K., et al. (2009). Next-generation sequencing technologies and their applications for crop genetics and breeding. Trends in Biotechnology, 27(9), 522-530.
49. Vareed, S.K., et al. (2008). Pharmacokinetics of curcumin conjugate metabolites in healthy human subjects. Cancer Epidemiology Biomarkers & Prevention, 17(6), 1411-1417.
50. Voytas, D.F. (2013). Plant genome engineering with sequence-specific nucleases. Annual Review of Plant Biology, 64, 327-350.
51. Wang, M.L., et al. (2011). Genetic mapping and QTL analysis of ginger for agronomic and therapeutic traits. Plant Breeding, 130(4), 529-536.
52. Wang, Z., et al. (2009). RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1), 57-63.
53. Xu, W., et al. (2015). WRKY transcription factors: Key regulators of plant defense responses and curcumin biosynthesis in turmeric. BMC Plant Biology, 15, 157.
54. Zhang, L., et al. (2019). Development of transdermal delivery systems for curcumin. Drug Development and Industrial Pharmacy, 45(3), 374-382.
55. Zhang, Y., et al. (2020). Genetic engineering of curcumin synthase to enhance curcumin production in turmeric. Biotechnology Advances, 39, 107376.
Citation
APA Style
Ishola, O., Onyemaobi, U., Bello, H. B., Ayomide, I. P., Simon, G. O., Adesona, O. J., & Aremu, W. T. (2025). Development of a Python-Based pipeline for identifying Curcumin-Related genetic markers in Curcuma longa. International Journal of Scholarly Resources, 17(2).