Application of RAPD Molecular Technique to Study the Genetic Variations of Citrus in South Sulawesi, Indonesia

Mustika Tuwo (1), Tutik Kuswinanti (2), Andi Nasruddin (3), Elis Tambaru (4)
(1) Doctoral Program of Agricultural Science, Graduate School, Hasanuddin University, Makassar 90245, Indonesia
(2) Department of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar 90245, Indonesia
(3) Department of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar 90245, Indonesia
(4) Department of Biology, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia
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Tuwo, Mustika, et al. “Application of RAPD Molecular Technique to Study the Genetic Variations of Citrus in South Sulawesi, Indonesia”. International Journal on Advanced Science, Engineering and Information Technology, vol. 12, no. 6, Nov. 2022, pp. 2499-06, doi:10.18517/ijaseit.12.6.17066.
Indonesia is a tropical country with superior local citrus species and varieties. Citrus fruits were very useful for cultivation, especially to meet the nutritional needs of the wider community. A province in Indonesia, namely South Sulawesi is one of the centers for citrus development. A preliminary study showed various cultivated citrus in South Sulawesi namely Mandarin Orange cultivar Selayar, Mandarin Orange cultivar Batu, JC lime, Pummelo Pangkep, tangerine, Santang Madu, Dekopon, lime, and Kaffir lime. This study aims to evaluate genetic diversity at several citrus plantation centers in South Sulawesi using the RAPD technique. The analysis was carried out using five primers. In this study, RAPD primers could be used to characterize the genetic diversity and similarity of thirteen citrus cultivars in South Sulawesi. One informative RAPD primer based on its PIC value was OPC-09. The results of the genetic similarity analysis are presented in the form of a dendrogram. The first cluster consisted of Mandarin Orange cultivar Selayar (Seeded Selayar, Selayar-Selayar, JC-Selayar), JC lime, Mandarin Orange cultivar Batu, Santang Madu, and Pummelo Pangkep (cultivar Pangkep Merah, Pangkep Putih, Pangkep Golla-golla). The second cluster consisted of Mandarin Orange cultivar Selayar (selayar-selayar, JC-selayar), Santang Madu, tangerine, Mandarin Orange cultivar Batu, Dekopon, lime, and Kaffir lime. The clusters with the most distant genetic relationship are cluster A with cluster B, with a genetic similarity of 62%. Meanwhile, clusters with the closest genetic relationship are clusters I and II, with 79% genetic similarity.

Maskun, H. Assidiq, N. H. Al Mukarramah, and S. N. Bachril, “Threats to the sustainability of biodiversity in Indonesia by the utilization of forest areas for national strategic projects: A normative review,” in IOP Conf. Series: Earth and Environmental Science, UK, 2021, pp. 1-9.

United Nations Group of Experts on Geographical Names, Country report of the Republic of Indonesia. Geospatial Information Agency of Indonesian, 2019, Accessed on: Jan. 24, 2022. [Online] Available: https://unstats.un.org/unsd/geoinfo/UNGEGN/docs/1st-session/GEGN.2_2019_CRP.132_Country_Report_Indonesia_2019.pdf.

J. P. T. Kumar, A. Thirugnavel, D. Y. Upadhyay, S. A. Kamde, P. R. Jalamkar, and A. A. Murkute, “Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel Markers, ” bioRxiv., 2022.

Y. G. D. Anggraheni, E. S. Mulayaningsih, and D. Priadi, “Genetic variability of Citrus spp. in Cibinong germplasm garden using random amplified polymorphic DNA,” in IOP Conf. Series: Earth and Environmental Science., UK, 2021, pp. 1-9.

A. Tolangara, A. D. Corebima, A. Mas’ud, and Sundari, “Genetic diversity of Lemon(Citrus spp.) from Ternate island (Indonesia) based on morphological and molecular characterization,’ Biodiversitas., vol. 21, no. 5, pp. 1908-1913, May 2020.

C. Liu, H. Liu, J. Hurst, M. P. Timko, and C. Zhou, “Recent advances on citrus yellow vein clearing virus in citrus,” Horticultural Plant Journal., vol. 6, no. 4, pp. 216-222, July 2020.

G. D. Vita, M. Borrello, R. Vecchio, G. Gulisano, and M. D’Amico, “Purchasing drivers of fresh citrus fruits in urban Italy: is it all about taste?”, Nutrients., vol. 12, pp. 1-10, April 2020.

R. Visvanathan and G. Williamson, “Effect of citrus fruit and juice consumption on risk of developing type 2 diabetes: evidence on polyphenols from epidemiological and intervention studies,” Trends in Food Science & Technology., vol. 115, pp. 133-146, Sept. 2021.

I. Jevtic, D. I. Udovicic, M. Ljubica, and A. Matic, “The Possibility of satisfying vitamin C daily needs by consuming fresh orange and grapefruit,” Journal of Hygienic Engineering and Design, pp. 52-57, 2019.

P. Inglese and G. Sortino, “Citrus history, taxonomy, breeding, and fruit quality”, in Research Paper - University of Oxford. Oxford University Press USA: Oxford Research Encyclopedia of Environmental Science, 2019, pp. 1-22. [Online] Available: https://www.researchgate.net/publication/331399212_Citrus_History_Taxonomy_Breeding_and_Fruit_Quality_Citrus_History_Taxonomy_Breeding_and_Fruit_Quality_Summary_and_Keywords.

M. Kim, S. H. Kim, H. B. Kim, Y. C. Park, and K. J Song, “Some factors affecting the efficiency of hybrid embryo rescue in the ‘Shiranuhi’ mandarin,” Horticultural Science and Technology., vol. 38, pp. 271-281, Jan. 2020.

J. Singh, V. Sharma, K. Pandey, S. Ahmed, M. Kaur and G. S. Sidhu, “Horticultural classification of citrus cultivars”, Intechopen, 2021, pp. 1-24. [Online] Available: https://www.researchgate.net/publication/331399212_Citrus_History_Taxonomy_Breeding_and_Fruit_Quality_Citrus_History_Taxonomy_Breeding_and_Fruit_Quality_Summary_and_Keywords.

V. Zech-Matterne and G. Fiorentino, “Archaeology and history of citrus fruit in the mediterranean: acclimatization, diversifications, uses. Publications du Centre Jean Bí©rard: Naples. 2018.

H. Zainuri and K. Yamaura, “New farmers’ incentives under the new tangerine farming support: the case of Tuban, Indonesia,” International Journal of Fruit Science., vol. 21, pp. 392-399, Mar. 2021.

Balitjestro, Types of Oranges Growing in Indonesia. 2020. Accessed on: Jan. 26, 2022. [Online] Available: http://balitjestro.litbang.pertanian.go.id/jenis-jeruk-yang-berkembang-di-indonesia/.

M. Addi, A. Elbouzidi, M. Abid, D. Tungmunnithum, A. Elamrani and C. Hano, “An overview of bioactive flavonoids from citrus fruits,” An Overview of Bioactive Flavonoids from Citrus Fruits., vol. 12, pp. 1-15, Dec. 2021.

R. Chen, K. Takamura, K. Sugiyama, D. Kami, K. Shimomura, and Y. Yoshioka, “Genetic diversity assessment of Cucurbita genetic resources in Japan by nuclear and organelle DNA markers,” The Horticulture Journal., vol. 90, pp. 382-392, July 2021.

R. Herawati, Alnopri, Masdar, U. K. Joko, and B. G. Murcitro, “Assessment of genetic diversity in various yield traits to determinea high yielding new type of upland rice,” International Journal on Advanced Science Engineering Information Technology., vol. 11, pp. 828-833, Apr. 2021.

A. F Yusuf and B. S. Daryono, “Studies of genetic and morphological characteristics of indonesian melon (Cucumis melo L. ‘Hikapel’) germplasm,” International Journal on Advanced Science Engineering Information Technology., vol. 11, pp. 2023-2030, Oct. 2021.

F. Akohoue, E. G. Achigan-Dako, C. Sneller, A. V. Deynze, and J. Sibiya, “Genetic diversity, SNP-trait associations and genomic selection accuracy in a west african collection of Kersting’s groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet],” Plos One., vol. 15, pp. 1-24, Jun. 2020.

M. A. Sihalohoa, D. S. Hanafiab, E. Juliantic, and M. Basyuni, “Morphological characters of local origin durian (Durio zibethinus Murr.) fruits and seeds from Central Tapanuli Regency, North Sumatra, Indonesia,” International Journal on Advanced Science Engineering Information Technology., vol. 11, pp. 213-222, Feb. 2021.

Kristamtini, S. Widyayanti and H. Purwaningsih, “Genetic diversity of local red rice cultivars collections of Yogyakarta AIAT, Indonesia based on morphological character,” in IOP Conf. Series: Earth and Environmental Science, UK, 2020, pp. 1-6.

F. Yulianti, A. L. Adiredjo, L. Soetopo, and S. Ashari, ”Morphology and genetic characteristics of potential citrus rootstock in Indonesia,” Biodiversitas., vol. 21, pp. 5514-5520, Nov. 2020.

F. P. Sabdanawaty, Purnomo, and B. S. Daryono,”Species diversity and phenetic relationship among accessions of api-api (Avicennia spp.) in Java based on morphological characters and ISSR markers,” Biodiversitas., vol.22, pp. 193-198, Jan. 2021.

G. R. Aristya, R. Kasiamdari, M. F. Arif, F. Amalia, and R. D. Pawestri, “Comparison of molecular markers ISSR, SSR and RFLP to study the genetic variation of strawberry cultivars,” American Journal of Agricultural and Biological Science., vol. 14, pp. 61-68, Mar. 2019.

S. Amiteye, “Basic concepts and methodologies of DNA marker systems in plant molecular breeding,” Heliyon., vol. 7, pp. 1-20, Sep. 2021.

M. R. Pahlevi, S. Indriyani, R. Mastuti, and E. L. Arumingtyas, “Genetic variation based on RAPD profiling and production loss of cayenne pepper due to periodic flooding,” International Journal on Advanced Science Engineering Information Technology., vol. 11, pp. 834-842, Apr. 2021.

M. Cehula, J. Mlcek, T. Jurí­koví¡, J. Žiarovskí¡, O. Paulen, L. Dokoupil, A. Adí¡mkoví¡, and R. Babosova, “Assessment of genetic diversity of edible honeysuckle monitored through RAPD in relative to bioactive substances,” Agronomy., vol. 10, pp. 1-11, Jun. 2020.

D. Yuan, H. Qin, D. Chen, and J. Chen, “Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD,” BMC Infectious Diseases., vol. 21, pp. 1-10, May 2021.

I. B. K. Mahardika, I. N. Rai, M. S. Mahendra, and R. Dwiyani, “Genetic diversity and fruit qualityof several pomelo “Jeruk Bali”(Citrus grandis L. Osbeck) cultivars in Bali,” International Journal of Bioscience and Biotechnology., vol. 5, no. 1, pp. 43-59. Sept. 2017.

M. Tuwo, T. Kuswinanti, A. Nasruddin, and E. Tambaru, “RAPD primer screening as a preliminary study to analyze the genetic diversity of Citrus spp. in South Sulawesi,” in IOP Conf. Series: Earth and Environtmental Science, UK, 2021, pp. 1-7.

R. S. Kasiamdari, G. R. Aristya, H. Prabowo, C. Ariesta, and M. F. Arif, “Genetic diversity of Indonesian’s sugarcane varieties (Saccharum officinarum) based on RAPD molecular markers,” Biodiversitas., vol. 20, pp. 3005-3010, Oct. 2019.

Uslan and M. Pharmawat, “Genetic diversity of Sterculia quadrifida in Kupang, Indonesia based on RAPD (Random Amplified Polymorphic DNA) markers,” Biodiversitas., vol. 21, pp. 3407-3414, Jul. 2020.

L. Wallace, “Methods available for the analysis of data from dominant molecular markers. Department of Biology,” University of South Dakota, 2003.

Z. H. Guo, K. X. Fu, X. Q. Zhang, S. Q. Bai, Y. Fan, Y. Peng, L. K. Huang, Y. H. Yan, W. Liu, and X. Ma, “Molecular insights into the genetic diversity of Hemarthria compressa germplasm collections native to Southwest China,” Molecules., vol. 19, no. 12, pp. 41-59, Dec. 2014.

D. Botstein, R. L. White, M. Skolnick, and R. W. Davis, “Construction of a genetic linkage map in man using restriction fragment length polymorphisms,” Am. J. Hum. Genet., vol. 32, pp. 314-331, May 1980.

H. Sadiyah, S. Ashari, B. Waluyo, and A. Soegianto, “Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers,” Biodiversitas., vol. 22, pp. 184-192, Jan. 2021.

Lizawati, S Nusifera, Neliyati, Y Alia and Antony, “RAPD-PCR primer selection to analyze genetic diversity of Cinnamon plan,” in IOP Conf. Series: Earth and Environmental Science, UK, 2021, pp. 1-7.

J. G. Williams, A. R. Kubelik, K. J. Livak, K. J. Rafalski, and S. V. Tingey, “DNA polymorphisms amplified by arbitrary primers are useful as genetic markers,” Nucleic Acid Research., vol. 18, no. 22, pp. 6531-6535, Nov. 1990.

Annisa, R. Hafzari, T. Setiawati, B. Irawan, and J. Kusmoro, “Evaluation of RAPD markers for molecular identification of five bamboo genera from Indonesia,” Folia Forestalia Polonica., vol. 61, no. 4, pp. 255-266, Dec. 2019.

J. Normala, V. T. Okomada, A. A. Mohd, A. A. Nur, A. B. Abol-Munafi, and S. Md. Sheriff. “Genetic variation between triploid and diploid Clarias gariepinus (Burchell, 1822) using RAPD markers,” Veterinary Sciences., vol. 8, no. 75, pp. 1-12, May 2021.

S. R. Dalimunthe, L. A. M. Siregar, L. A. P. Putri, T. Chairunnisa, and A. Hairmansis, “Polymorphism levels of some SSR markers (Simple Sequence Repeat) for parental line identification on low temperature tolerance,” in IOP Conf. Series: Earth and Environmental Science, UK, 2020, pp. 1-9, 2020.

Serrote, C. M. Lemos, Reiniger, L. Silveira, Rejane, Silva, K. Buuron, Rabaiolli, S. M. Santos, Stefanel, and C. Moro, “Determining the polymorphism information content of a molecular marker,” Journal pre-proofs., Elsevier. 2019.

A. S. Shaibu, H. Ibrahim, Z. L. Miko, I. B. Mohammed, S. G. Mohammed, H. L. Yusuf, A. Y. Kamara, L. O. Omoigui, and B. Karikari, “Assessment of the genetic structure and diversity of soybean (Glycine max L.) germplasm using diversity array technology and single nucleotide polymorphism markers,” Plants., vol.11, pp. 1-13, D2022.

Z. Luo, J. Brock, J. M. Dyer, T. Kutchan, D. Schachtman, M. Augustin, Y. Ge, N. Fahlgren, and H. Abdel-Haleem, “Genetic diversity and population structure of a Camelina sativa spring panel,” Frontiers in Plant Science, vol. 10, no. 184, pp. 1-12, Feb. 2019.

Q. B. Zhao, H. Sun, Z. Zhang, Z. Xu, B. S. Olasege, P. P. Ma, X. Z. Zhang, Q. S. Wang, and Y. C. Pan, ”Exploring the structure of haplotype blocks and genetic diversity in chinese indigenous pig populations for conservation purpose,” Evolutionary Bioinformatics., vol. 15, pp. 1-8, Jan. 2019.

Siregar, U. Juniarti, and R. D. Olivia, “Genetic Diversity of Sengon (Paraserianthes falcataria (L)) in Java Community Forest based on RAPD Marker,” Journal of Tropical Silviculture., vol. 3, pp. 1-7, Feb. 2012.

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