Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers
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Abstract. Boonsrangsom T, Fuenghoi C, Premjet D, Suvittawat K, Ratanasut K, Sujipuli K. 2023. Genetic relationships and genome verification of Thai banana cultivars using Random Amplification of Polymorphic DNA (RAPD) markers. Biodiversitas 24: 3758-3765. Edible bananas and plantains, belonging to the family Musaceae, genus Musa, represent one of the most important fruit crops, with an annual production of more than 65 million tons worldwide. Bananas have several hybrid variations since they are descended from the two species Musa acuminata Colla (AA genome) and Musa balbisiana Colla (BB genome). Different morphological traits divide almost hybrid bananas into various genomic groupings. Banana genome categorization and identification, however, have always been challenging issues. This study aimed to assess the genetic relationships and verify the genomes of Thai banana cultivars using random amplification of polymorphic DNA (RAPD) markers. Using the 15 selected RAPD markers, 149 RAPD bands were found, with sizes ranging from 0.2 to 3.2 kb, and 88.6% were polymorphic. Polymorphic information content (PIC) values ranged from 0.18 to 0.42, averaging 0.30. Based on the Jaccard coefficient, the unweighted pair-group method arithmetic average (UPGMA) analysis showed that the banana samples had a similarity range of 0.27 to 1.00 with a mean of 0.56, demonstrating an abundance of viability across six banana genomes. The dendrogram generated from RAPD data revealed that all 18 Musa samples could be divided into two main groups (Group I and II). Three additional subgroups were created for each primary group (A, B, and C). The accurate identification and genetic data on the available genetic resources for bananas will be beneficial for breeding and conservation programs.
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References
Agarwal M, Shrivastava N, Padh H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27 (4): 617-631. DOI: 10.1007/s00299-008-0507-z.
Amiteye S. 2021. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 7 (10): e08093. DOI: 10.1016/j.heliyon.2021.e08093.
Atom AD, Lalrinfela P, Thangjam R. 2015. Genome classification of banana genetic resources of Manipur using morphological characters. Sci Vis 15 (4): 189-195.
Babu AG, Prabhuling G, Karani RS, SATISH D, Patil RK, Mulla SR, Raghavendra G, Jagadeesha RC. 2018. Genetic diversity analysis among banana cultivars through ISSR markers. J Pharmacogn Phytochem 7 (6): 1576-1580.
Bakry F, Carreel F, Jenny C, Horry JP. 2009. Genetic improvement of banana. In: Jain SM, Priyadarshan PM (eds) Breeding plantation tree crops: tropical species. Springer, New York. DOI: 10.1007/978-0-387-71201-7_1.
Boonsrangsom T, Phetnin B, Ratanasut K, Sujipuli K. 2020. Assessment of genetic diversity among Musa cultivars based on sequence-related amplified polymorphism technique. Naresuan Univ J Sci Technol 28 (2): 52-61. DOI:10.14456/nujst.2020.15.
Boonsrangsom T. 2020. Genetic diversity of 'Wan Chak Motluk' (Curcuma comosa Roxb.) in Thailand using morphological characteristics and random amplification of polymorphic DNA (RAPD) markers. S Afr J Bot 130: 224-230. DOI: 10.1016/j.sajb.2020.01.005.
Brake M, Migdadi HM, Al-Gharaibeh MA, Ayoub S, Haddad NJ, Oqlah AA. 2014. Characterization of Jordanian olive cultivars (Olea europaea L.) using RAPD and ISSR molecular markers. Sci Hortic 176: 282-289. DOI: 10.1016/J.SCIENTA.2014.07.012.
Epe IA, Bir MSH, Choudhury AK, Khatun A, Aktar MM, Arefin MS, Islam MA, Park KW. 2021. Genetic diversity analysis of high yielding rice (Oryza sativa) varieties cultivated in Bangladesh. Korean J Agric Sci 48: 283-297. DOI: 10.7744/kjoas.20210022.
Felbinger C, Kutzsche F, Mönkediek S, Fischer M. 2020. Genetic profiling: differentiation and identification of hazelnut cultivars (Corylus avellana L.) using RAPD-PCR. Food Control 107: 106791. DOI: 10.1016/J.FOODCONT.2019.106791.
Guo ZH, Fu KX, Zhang XQ, Bai SQ, Fan Y, Peng Y, Huang LK, Yan YH, Liu W, Ma X. 2014. Molecular insights into the genetic diversity of Hemarthria compressa germplasm collections native to southwest China. Molecules (Basel, Switzerland) 19 (12): 21541-21559. DOI: 10.3390/molecules191221541.
Hampl V, Pavlícek A, Flegr J. 2001. Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program Free Tree: Application to trichomonad parasites. Intl J Syst Evol Microbiol 51 (3): 731-735. DOI: 10.1099/00207713-51-3-731.
Hapsoro D, Warganegara H, Utomo S, Sriyani N, Yusnita Y. 2015. Genetic diversity among sugarcane (Saccharum officinarum L.) genotypes as shown by randomly amplified polymorphic DNA (RAPD). Agrivitas J Agric Sci 37 (3): 247-257. DOI: 10.17503/agrivita.v37i3.499.
Hasanah Y, Mawarni L, Hanu H, Lestami A. 2022. Genetic diversity of shallots (Allium ascalonicum L.) from several locations in North Sumatra, Indonesia based on RAPD markers. Biodiversitas 23: 2405-2410. DOI: 10.13057/biodiv/d230518.
Hinge VR, Shaikh IM, Chavhan RL, Deshmukh AS, Shelake RM, Ghuge SA, Dethe AM, Suprasanna P, Kadam US. 2022. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci Rep 12 (1): 7979. DOI: 10.1038/s41598-022-11992-1.
Igwe DO, Ihearahu OC, Osano AA, Acquaah G, Ude GN. 2022. Assessment of genetic diversity of Musa species accessions with variable genomes using ISSR and SCoT markers. Genet Resour Crop Evol 69: 49-70. DOI: 10.1007/s10722-021-01202-8.
Jaccard P. 1908. Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44: 223-270.
Kabir MH, Mamun ANK, Fatema H, Amin R. 2015. Assessment of genetic diversity in 13 local banana (Musa spp.) cultivars using simple sequence repeat (SSR) markers. Intl J Rec Res Life Sci 2 (1): 65-69.
Kanjanaphachoat P, Topoonyanont N, Jantawichai P. 2020. RAPD marker analysis of genetic variation in Kluai Nam Wa (Musa ABB group) banana plants regenerated after 8 and 9 subcultures. Maejo Intl J Sci Technol 14 (2): 130-140.
Kumari N, Thakur SK. 2014. Randomly amplified polymorphic DNA - a brief review. Am J Anim Vet Sci 9 (1): 6-13. DOI: 10.3844/ajavsp.2014.6.13.
Kundu P, Bauri FK, Maji S. 2018. Genetic diversity study of some banana genotypes collected from various parts of India through RAPD analysis. Afr J Agric Res 13: 248-257. DOI: 10.5897/AJAR2015.10350.
Mir MA, Mansoor S, Sugapriya M, Alyemeni MN, Wijaya L, Ahmad P. 2021. Deciphering genetic diversity analysis of saffron (Crocus sativus L.) using RAPD and ISSR markers. Saudi J Biol Sci 28 (2): 1308-1317. DOI: 10.1016/j.sjbs.2020.11.063.
Niklas A, Olszewska D. 2021. Application of the RAPD technique to identify genetic diversity in cultivated forms of Capsicum annuum L. Biotechnol 102 (2): 209-223. DOI: 10.5114/bta.2021.106523.
Oliya BK, Chand K, Thakuri LS, Baniya MK, Sah AK, Pant B. 2021. Assessment of genetic stability of micropropagated plants of Rhynchostylis retusa (L.) using RAPD markers. Sci Hortic 281: 110008. DOI: 10.1016/J.SCIENTA.2021.110008.
Poerba YS, Ahmad F. 2010. Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas 11 (3): 118-123. DOI: 10.13057/biodiv/d110303.
Pradhan S, Paudel YP, Qin W, Pant B. 2023. Genetic fidelity assessment of wild and tissue cultured regenerants of a threatened orchid, Cymbidium aloifolium using molecular markers. Plant Gene 34: 100418. DOI: 10.1016/j.plgene.2023.100418.
Premjet D, Boonsrangsom T, Sujipuli K, Rattanasut K, Kongbangkerd A, Premjet S. 2022. Morphological and molecular characterizations of Musa (ABB) 'Mali-Ong' in Thailand. Biology 11 (10): 1429. DOI: 10.3390/biology11101429.
Rao GK, Kapadia C, Patel NB, Desai KD, Narasimha Murthy PN. 2020. Genetic diversity analysis of greater yam (Dioscorea alata L.) genotypes through RAPD and ISSR markers. Biocatal Agric Biotechnol 23: 101495. DOI: 10.1016/j.bcab.2020.101495
Safhi FA, Alshamrani SM, Alshaya DS, Hussein MAA, Abd El-Moneim D. 2023. Genetic diversity analysis of banana cultivars (Musa sp.) in Saudi Arabia based on AFLP marker. Curr Issues Mol Biol 45 (3): 1810-1819. DOI: 10.3390/cimb45030116.
Sahu PK, Sao R, Mondal S, Vishwakarma G, Gupta SK, Kumar V, Singh S, Sharma D, Das BK. 2020. Next generation sequencing based forward genetic approaches for identifcation and mapping of causal mutations in crop plants: a comprehensive review. Plants 9: 1355. DOI: 10.3390/plants9101355.
Shelke RG, Das AB. 2015. Analysis of genetic diversity in 21 genotypes of Indian banana using RAPDs and IRAPs markers. Proc Natl Acad Sci, India Sect B Biol Sci 85 (4): 1027-1038. DOI: 10.1007/s40011-015-0505-1
Silayoi B. 2015. Banana. Kasetsart University Publishing, Bangkok, 512 p. [Thai]
Simmonds NW, Shepherd K. 1955. The taxonomy and origins of the cultivated bananas. Bot J Linn Soc 55 (359): 302-312. DOI: 10.1111/j.10958339.1955.tb00015.x.
Smith JS, Chin EC, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J. 1997. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree. Theor Appl Genet 95: 163-173. DOI: 10.1007/s001220050544.
Singh WA, Singh NS, Devi EJ, Handique PJ, Devi HS. 2021. Collection and characterization of banana gene pools (Musa spp.) in Manipur (N.E. India) using PCR-RFLP and RAPD and ISSR markers. Braz J Bot 44: 671-684. DOI: 10.1007/s40415-021-00722-y.
Statista. 2021. Banana production worldwide by region. https://www.statista.com/statistics/264003/production-of-bananas-worldwide-by-region/
Sunaryo W, Mulyadi A, Nurhasanah. 2019. Genome group classification and diversity analysis of talas and rutai banana, two local cultivars from East Kalimantan, based on morphological characters. Biodiversitas 20: 2355-2367. DOI: 10.13057/biodiv/d200834.
Sunaryo W, Wahida, Idris SD, Pratama AN, Ratanasut K, Nurhasanah. 2020. Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers. Biodiversitas 21: 824-832. DOI: 10.13057/biodiv/d210250.
Tung PHT, Van T, Huong PT. 2022. Assessment of genetic variation of the genus Gymnema in Vietnam, using RAPD and ITS-rDNA markers. J Herbs Spices Med 28 (3): 281-292. DOI: 10.1080/10496475.2022.2058672.
Valmayor RV, Jamaluddin SH, Silayoi B, Kusumo S, Danh LD, Pascua OC, Espino RRC. 2000. Banana Cultivar Names And Synonyms In Southeast Asia. International Network for Improvement of Banana and Plantain-Asia and the Pacific Office, Laguna (Philippines).
Wahyudi D, Rifliyah K, Uslan. 2020. Genome evaluation of banana cultivars based on morphological character and inter-simple sequence repeat (ISSR) molecular marker. Biodiversitas 21: 2982-2990. DOI: 10.13057/biodiv/d210715.
Wongniam S, Somana J, Swangpol SC, Seelanan T, Chareonsap PP, Chadchawan S, Jenjittikul T. 2010. Genetic diversity and species-specific PCR-based markers from AFLP analyses of Thai bananas. Biochem Syst Ecol 38: 416-427. DOI: 10.1016/J.BSE.2010.03.015.
Youssef M, Escobedo-GraciaMedrano RM. 2016. Genetic relationship among Musa balbisiana accessions and identification of SRAP markers linked to Musa B genome. J Agric Chem Biotechnol 7 (2): 39-47.
Zozimo ROB, Ratanasut K, Boonsrangsom T, Sujipuli K. 2018. Assessment of genetic diversity among Thai banana cultivars (Musa spp.) based on RAPD and SRAP markers. Intl J Biosci 12 (4): 172-180. DOI: 10.12692/ijb/12.4.172-180.
Zulfahmi, Pertiwi SA, Rosmaina, Elfianis R, Gulnar Z, Zhaxybay T, Bekzat M, Zhaparkulova G. 2023. Molecular identification of mother trees of four matoa cultivars (Pometia pinnata Forst & Forst) from Pekanbaru City, Indonesia using RAPD markers. Biodiversitas 24: 1524-1529. DOI: 10.13057/biodiv/d24032.
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