* Corresponding Author
Genetic Diversity of Elephant Foot Yam (Amorphophallus paeoniifolius) and Two Other Relatives from the Meratus Mountains of South Kalimantan, Indonesia
https://doi.org/10.22146/jtbb.66231 Dindin Hidayatul Mursyidin(1*), Muhammad Aldy Hernanda(2), Badruzsaufari Badruzsaufari(3)
(1) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat, South Kalimantan, 70714 Indonesia
(2) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat, South Kalimantan, 70714 Indonesia
(3) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat, South Kalimantan, 70714 Indonesia
(*) Corresponding Author
Abstract
Elephant foot yam (Amorphophallus paeoniifolius) is a tuber crop with high economic value, so it is very prospective to be developed. This study aimed to characterize and determine the genetic diversity and relationship of A. paeoniifolius and two other relatives from the Meratus Mountains of South Kalimantan, Indonesia, using the rbcL marker. Eight samples of A. paeoniifolius and three other ones (outgroups), two of A. muelleri and one of A. borneensis, were used in the study. The genetic diversity was determined using the nucleotide diversity index (π), whereas the phylogenetic relationships were reconstructed using the Maximum Likelihood (ML) and Neighbor-Joining (NJ) methods. The results show that this germplasm has a high diversity at an inter-species level of 0.95% and a low at intra-species (0.33%). The phylogenetic analyses revealed that Amorphophallus from this region separated into different clades, three for NJ and one for ML. In this case, A. paeoniifolius var. sylvestris from Bati-Bati, Tanah Laut is closely related to A. paeoniifolius var. hortensis from Marajai, Balangan. In conclusion, although Amorphophallus from the Meratus Mountains of South Kalimantan, Indonesia, shows a high diversity at an inter-species level, the phylogenetic analyses revealed a unique relationship. This finding is expected to be a reference in supporting efforts to conserve, cultivate, and utilize sustainable Amorphophallus, globally and locally, particularly for the Dayak Meratus community of the South Kalimantan, Indonesia.
Keywords
Full Text:
PDFReferences
Aloqalaa, D.A. et al., 2019. The impact of the transversion/transition ratio on the optimal genetic code graph partition. Proceeding of International Conference in Bioinformatics Models, Methods and Algorithms, Prague, Czech Republic, pp.55–65.
Acquaah, G., 2017. Plant breeding, principles. In: Encyclopedia of applied plant science. Second edition, Elsevier Inc.: New York, USA.
Bhandari, H.R. et al., 2017. Assessment of genetic diversity in crop plants: An overview. Advance of Plants Agriculture Research, 7, pp.279–286. doi: 10.15406/apar.2017.07.00255.
CBOL, 2009. A DNA barcode for land plants. Proceedings of National Academy of Science 106(31), pp.12794–12797. doi: 10.1073/pnas.0905845106.
Chandrasekara, C.H.W.M.R.B. et al., 2021. Universal barcoding regions, rbcL, matK and trnH-psbA do not discriminate Cinnamomum species in Sri Lanka. PLoS ONE, 16(2), pp.1-16. doi: 10.1371/journal.pone.0245592.
Dean, G.H. et al. 2018. Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia. Application in Plant Sciences, 6(7), pp.1-12. doi: 10.1002/aps3.1167.
Dong, L.N. et al., 2011. Efficiency of DNA barcodes for species delimitation: A case in Pterygiella Oliv. (Orobanchaceae). Journal of Systematics and Evolution, 49(3), pp.189–202. doi: 10.1111/j.1759-6831.2011.00124.x.
Dong, Z. et al., 2013. Phylogeny and molecular evolution of the rbcL gene of St genome in Elymus sensu lato (Poaceae : Triticeae). Biochemistry and Systematics Ecology, 50, pp.322–330. doi: 10.1016/j.bse.2013.05.005.
Felsenstein, J., 1985. Confidence-limits on phylogenies: An approach using the bootstrap. Evolution, 39, pp.783–791.
Gao, Y. et al., 2017. Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences. Mitochondrial DNA Part A, pp.1–8. doi: 10.1080/24701394.2017.1350855.
Gholave, A.R. et al., 2017. Reconstruction of molecular phylogeny of closely related Amorphophallus species of India using plastid DNA marker and fingerprinting approaches. Physiology and Molecular Biology of Plants, 23(1), pp.155–167. doi: 10.1007/s12298-016-0400-0.
Govindaraj, M., Vetriventhan, M. & Srinivasan, M., 2015. Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015, pp.1–14. doi: 10.1155/2015/431487.
Grob, G.B.J. et al., 2002. Phylogeny of the tribe Thomsonieae (Araceae) based on chloroplast matK and trnL intron sequences. Systematics Botany, 27(3), pp.453–467. doi: 10.1043/0363-6445-27.3.453.
Keller, I., Bensasson, D. & Nichols, R.A., 2007. Transition-transversion bias is not universal: A counter example from grasshopper pseudogenes. PLoS Genetics, 3, pp.0185–0191. doi: 10.1371/journal.pgen.0030022.
King, V.T., Ibrahim, Z. & Hassan, N.H., 2017. Borneo studies in history, society and culture, Springer Science+Business Media: Singapore.
Kumar, S. et al., 2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), pp.1547–1549. doi: 10.1093/molbev/msy096.
Larkin, M.A., et al., 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23, pp.2947-2948. doi: 10.1093/bioinformatics/btm404.
Lee, S.C. et al., 2017. DNA barcode and identification of the varieties and provenances of Taiwan’s s domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences. Journal of Food and Drug Analysis, 25, pp.260–274. doi: 10.1016/j.jfda.2016.06.008.
Liu, L. et al., 2012, Adaptive evolution of the rbcL gene in Brassicaceae. Biochemistry and Systematics Ecology, 44, pp.13–19. doi: 10.1016/j.bse.2012.04.007.
Malhotra, N. et al., 2018. Genetic resources: Collection, conservation, characterization, and maintenance. In: Lentils, Potential resource for enhancing genetic gains, Elsevier Inc., New York, pp.21–41. doi: 10.1016/B978-0-12-813522-8.00003-0.
Mekkerdchoo, O. et al., 2016. Tracing the evolution and economic potential of konjac glucomannan in Amorphophallus species (Araceae) using molecular phylogeny and RAPD markers. Phytotaxa, 282(2), pp.81–106. doi: 10.11646/phytotaxa.282.2.1.
Mursyidin, D.H., et al., 2018. Molecular diversity of tidal swamp rice (Oryza sativa L.) in South Kalimantan, Indonesia. Diversity, 10(22), pp.1–10. doi: 10.3390/d10020022.
Mursyidin, D.H., et al., 2021. DNA barcoding of the tidal swamp rice (Oryza sativa) landraces from South Kalimantan, Indonesia. Biodiversitas, 22(4), pp.1593–1599. doi: 10.13057/biodiv/d220401.
Nei, M., 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Nei, M., 2007. The new mutation theory of phenotypic evolution, PNAS, 104, pp.12235–12242. doi: 10.1073/pnas.0703349104.
Newmaster, S.G., Fazekas, A.J. & Ragupathy, S., 2006. DNA barcoding in land plants: Evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany, 84, pp.335–341. doi: 10.1139/b06-047.
Poerba, Y.S., Leksonowati, A. & Martanti, D., 2009. Effect of ethyl methanesulfonate (EMS) mutagens on the growth of Iles-Iles (Amorphophallus muelleri Blume) in vitro culture. Berita Biologi, 9(4), pp.419-425. doi: 10.14203/beritabiologi.v9i4.2013.
Ripley, L.S., 2013. Mutation. In Brenner’s Encyclopedia of Genetics: Second Edition. New York, USA.: Elsevier Inc., pp.534–539.
Sedayu, A. et al., 2010. Morphological character evolution of Amorphophallus (Araceae) based on a combined phylogenetic analysis of trnL, rbcL and LEAFY second intron sequences. Botanical Studies, 51, pp.473–490.
Singh, J. et al., 2017. Evaluation of potential DNA barcoding loci from plastid genome: Intraspecies discrimination in Rice (Oryza species). International Journal of Current Microbiology and Applied Sciences, 6, pp.2746–2756. doi: 10.20546/ijcmas.2017.605.308.
Singh, J. & Banerjee, S., 2018. Utility of DNA barcoding tool for conservation and molecular identification of intraspecies of rice genotypes belonging to Chhattisgarh using rbcL and matK gene sequences. Plant Architecture, 18, pp.69–75.
Stoltzfus, A. & Norris, R.W., 2015. On the causes of evolutionary transition: transversion bias. Molecular Biology and Evolution, 33, pp.595–602. doi: 10.1093/molbev/msv274.
Sunaryo, W., 2015. Application of DNA barcoding for genetic diversity analysis of lai-durian (Durio zibethinus x kutejensis) from East Kalimantan. Prosiding Seminar Nasional Masyarakat Biodiversitas Indonesia, 1(6), pp.1273-1277.
Ude, G.N. et al., 2019. Genetic diversity and DNA barcoding of yam accessions from Southern Nigeria. American Journal of Plant Sciences, 10, pp.179-207. doi: 10.4236/ajps.2019.101015.
Wattoo, J.I. et al., 2016. DNA barcoding: amplification and sequence analysis of rbcL and matK genome regions in three divergent plant species. Advance in Life Science, 4(1), pp.3-7.
DOI: https://doi.org/10.22146/jtbb.66231
Article Metrics
Abstract views : 2981
| 
views : 1776
Refbacks
- There are currently no refbacks.
Copyright (c) 2022 Journal of Tropical Biodiversity and Biotechnology
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Editoral address:
Faculty of Biology, UGM
Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
ISSN: 2540-9581 (online)