Genetic Variation and Phylogenetic Analysis of Indonesian Sugarcane (Saccharum officinarum L.) based on Internal Transcribed Spacer (ITS-nrDNA)
Main Article Content
Abstract
Sugarcane (Saccharum officinarum L.) is a crucial agricultural crop in global sugar production. Over the past decade (2010–2019), sugarcane production in Indonesia has experienced annual fluctuations, reaching its peak in 2013 with 35.5 million tons and declining to 27.7 million tons in 2019. Concurrently, Indonesia’s sugar production only met 38% of domestic demand, necessitating the development of superior sugarcane cultivars with high sucrose content and resistance to pests and diseases. The aim of this study was to identify and determine the relationship among three sugarcane cultivars in Indonesia using DNA barcoding and constructing a phylogenetic tree based on ITS nuclear ribosomal DNA sequences. The ITS region was amplified using the primers ITS1 and ITS4, yielding a final base pair length of 531 bp. The sequences were then analysed to construct a phylogenetic tree using Maximum-Likelihood (ML) and Bayesian Inference (BI) methods. Sequence analysis was also conducted to determine genetic distances, polymorphic sites, haplotype distributions and Principal Coordinate Analysis (PCoA). Phylogenetic tree construction grouped all cultivars into three distinct clades for both methods, with all three cultivars placed in the same clade with a bootstrap value of 94 for ML and a posterior probability of 1 for BI. Haplotype distribution showed that cultivars POJ and Pringu belonged to the same group, and PCoA analysis indicated no separation based on geographic origin, with some compositions similar to those of other countries such as Mexico, Taiwan and China.
Article Details
This work is licensed under a Creative Commons Attribution 4.0 International License.
References
Ali S E, Qin Y, Shengpeng W and Mohamed A F. (2021). More than sweet: A phytochemical and pharmacological review of sugarcane (Saccharum officinarum L.). Food Bioscience 44(PB): 101431. https://doi.org/10.1016/j.fbio.2021.101431
Aristya G R, Fauzana P, Rina S K and Arni M. (2020). DNA barcoding and phylogenetic analysis sugarcane (Saccharum officinarum L.) based on MatK (Maturase K) gene. Key Engineering Materials 840(KEM): 162–170. https://doi.org/10.4028/www.scientific.net/kem.840.162
Badan Pusat Statistik. (2023). Statistik tebu Indonesia [Indonesia sugar cane statistics] (Vol. 13). Jakarta: BPS RI/BPS-Statistics Indonesia.
Besse P. (2014). Nuclear ribosomal RNA genes: ITS region. In P. Besse (ed.), Molecular plant taxonomy: Methods in molecular biology (Vol. 1115). Totowa, NJ: Humana Press, 141–149. https://doi.org/10.1007/978-1-62703-767-9_7
De Mendonça Vilela M, Luiz E D B, Marie A V S, Nathalia D S, João P K, Guilherme M Q C, Danilo A S, Anete P D S, Paulo C G F, Clícia G, Claudio B C-S, Renato V and Michel V. (2017). Analysis of three sugarcane homo/homeologous regions suggests independent polyploidization events of Saccharum officinarum and Saccharum spontaneum. Genome Biology and Evolution 9(2): 266–278. https://doi.org/10.1093/gbe/evw293
Dinesh Babu, Kandhalu S, Vardhana J, Harunipriya P, Lakshmi K, Raju G and Thakku R R. (2022). A short review on sugarcane: Its domestication, molecular manipulations and future perspectives. Genetic Resources and Crop Evolution 69(8): 2623–2643. https://doi.org/10.1007/s10722-022-01430-6
FAO. (2021). World food and agriculture. Statistical yearbook 2021. Rome. https://doi.org/10.1016/S0140-6736(59)91820-3
Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, et al. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications 9(1): 1–10. https://doi.org/10.1038/s41467-018-05051-5
Irvine J. E. (1999). Saccharum species as horticultural classes. Theoretical and Applied Genetics 98(2): 186–194. https://doi.org/10.1007/s001220051057
Liu Z F, Xiu Q C, Lang L, Hsi W L, John G C and Jie L. (2017). DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PLoS ONE 12(4): 1–20. https://doi.org/10.1371/journal.pone.0175788
McDonald M J, Wei C W, Hsien D H and Jun Y L. (2011). Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biology 9(6): 1–12. https://doi.org/10.1371/journal.pbio.1000622
Medeiros C, Thiago W A B and Monalisa S C. (2020). Molecular diversity and genetic structure of Saccharum complex accessions. PLoS ONE 15(5): 1–17. https://doi.org/10.1371/journal.pone.0233211
Michel C I, Rachel S M, Yanille T and Jeanmaire M. (2016). The nuclear Internal Transcribed Spacer (ITS2) as a practical plant DNA barcode for herbal medicines. Journal of Applied Research on Medicinal and Aromatic Plants 3(3): 94–100. https://doi.org/10.1016/j.jarmap.2016.02.002
Nguyen L T, Heiko A S, Arndt V H and Bui Q M. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32(1): 268–274. https://doi.org/10.1093/molbev/msu300
Peakall R and Smouse P E. (2012). GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics 28(19): 2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Piperidis G, Piperedis N and D’Hont A. (2010). Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Molecular Genetics and Genomics 284(1): 65–73. https://doi.org/10.1007/s00438-010-0546-3
Ronquist F, Maxim T, Paul V D M, Daniel L A, Aaron D, Sebastian H, Bret L, Liang L, Marc A. S and John P H. (2012). Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539–542. https://doi.org/10.1093/sysbio/sys029
Rozas J, Albert, J. C. Sanchez-DelBarrio, Sara G, Pablo L, Sebastian E R and Alejandro S. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34(12): 3299–3302. https://doi.org/10.1093/molbev/msx248
Widyasari W B, Lilik K P, Muhammad R R R and Arinta R P. (2022). Historical notes, germplasm development, and molecular approaches to support sugarcane breeding program in Indonesia. Sugar Tech 24(1): 30–47. https://doi.org/10.1007/s12355-021-01069-0
Yang C F, Li T Y, Yang R L, Ge M Z, Chun Y Z and Wei Z W. (2016). Sequence characteristics and phylogenetic implications of the NrDNA Internal Transcribed Spacers (ITS) in protospecies and landraces of sugarcane (Saccharum officinarum L.). Sugar Tech 18(1): 8–15. https://doi.org/10.1007/s12355-014-0355-9
Yang S, Xueting L, Fei H, Yongji H, Xinlong L, Jiayun W, Qinnan W, Zuhu D, Rukai C and Muqing Z. (2018). A new method based on SNP of NrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum. PLoS ONE 13 (5): 1–12. https://doi.org/10.1371/journal.pone.0197458