Sains Malaysiana 53(7)(2024): 1605-1616

http://doi.org/10.17576/jsm-2024-5307-10

 

Assessment of Genetic Diversity and Relatedness of Local Banana (Musa spp.) Cultivars in Malaysia using Simple Sequence Repeat (SSR) Markers

(Penilaian Kepelbagaian Genetik dan Perkaitan Kultivar Pisang Tempatan (Musa spp.) di Malaysia menggunakan Penanda Ulangan Jujukan Ringkas (SSR))

 

AMER IZZAT SAMSUDIN*, SHARMILAH VETARYAN, HOOI WEI YENG & LEE YANG PING

 

Precision Agriculture and Genomics Department, FGV Innovation Centre, FGV R&D Sdn Bhd, 71760 Bandar Enstek, Negeri Sembilan, Malaysia

 

Diserahkan: 26 Januari 2024/Diterima: 27 Mei 2024

 

Abstract

Banana (Musa spp.) is an economically important crop widely consumed all over the world. Understanding the genetic diversity and relatedness between various banana cultivars is important to continuously improve its fruit characteristics, nutritional value, and disease resistance. This study aimed to develop a DNA fingerprinting panel using polymorphic simple sequence repeat (SSR) markers for the genetic characterisation of 11 banana cultivars in Malaysia. A total of 10 polymorphic SSR markers were developed into a multiplex PCR reaction and capillary electrophoresis to uniquely profile our collection of banana cultivars. The developed fingerprinting panel successfully amplified a total of 95 alleles, with 6 to 13 alleles per SSR marker. The average SSR marker polymorphic information content (PIC) value is 0.812, indicating the informativeness of the panel. Analysis of molecular variance (AMOVA) shows that 97% of the molecular variance from our banana collection is due to inter-variety genetic diversity, while the remaining 3% is due to intra-variety genetic diversity. A population structure analysis groups our collection of banana varieties according to the presence of at least one M. balbisiana (B) genome in their genetic makeup. The Cavendish variety, however, showed a distinct structure compared to the other cultivars. This SSR fingerprinting panel provides valuable insights into the genetic diversity and relatedness between banana cultivars in Malaysia. It has the potential to assist future banana breeding initiatives and serve as an effective quality control measure for verifying varieties in a tissue culture facility involved in banana planting materials production.

 

Keywords: Banana cultivars; DNA fingerprinting; genetic characterisation; polymorphic SSR markers

 

Abstrak

Pisang (Musa spp.) adalah tanaman ekonomi yang penting dan banyak dimakan di seluruh dunia. Memahami kepelbagaian genetik dan hubung kait antara kultivar pisang adalah penting bagi terus menambahbaik ciri buahnya, nilai nutrisinya dan ketahanannya terhadap penyakit. Kajian ini bertujuan untuk membangunkan satu panel pencapjarian DNA menggunakan penanda ulangan jujukan ringkas (SSR) untuk pencirian genetik 11 kultivar pisang di Malaysia. Sejumlah 10 penanda SSR yang polimorfisme dibangunkan dalam tindak balas PCR multipleks yang dipadankan dengan elektroforesis kapilari bagi menentukan profil kumpulan kultivar pisang kami. Panel pencapjarian DNA yang dibangunkan ini berjaya mengamplifikasi secara keseluruhannya 95 alel, dengan jumlah 6 hingga 13 alel bagi setiap penanda SSR. Nilai purata kandungan maklumat polimorfik (PIC) bagi penanda SSR adalah 0.812, menunjukkan kebergunaan maklumat panel tersebut. Analisis variasi molekul (AMOVA) menunjukkan bahawa 97% variasi molekul daripada koleksi pisang kami adalah disebabkan oleh kepelbagaian genetik antara varieti, manakala baki 3% lagi adalah disebabkan oleh kepelbagaian genetik dalam varieti. Analisis struktur populasi mengumpulkan koleksi varieti pisang kami berdasarkan kehadiran sekurang-kurangnya satu genom M. balbisiana (B) dalam kandungan genetik mereka. Varieti Cavendish pada masa yang sama menunjukkan struktur yang berbeza apabila dibandingkan dengan kultivar lain. Panel pencapjarian SSR ini memberikan maklumat berharga tentang kepelbagaian genetik dan hubung kait antara kultivar pisang di Malaysia. Selain itu, panel ini berpotensi digunakan untuk membantu program biak baka pisang. Ia juga boleh digunakan sebagai salah satu alat kawalan kualiti untuk pengesahan varieti di fasiliti kultur tisu yang terlibat dalam pengeluaran bahan tanaman pisang.

 

Kata kunci: Kepelbagaian genetik; kultivar pisang; penanda SSR polimorfisme; pencapjarian DNA

 

RUJUKAN

Botstein, D., White, R.L., Skolnick, M. & Davis, R.W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32(3): 314-331.

Castellana, S., Ranzino, L., Beritognolo, I., Cherubini, M., Luneia, R., Villani, F. & Mattioni, C. 2020. Genetic characterization and molecular fingerprint of traditional Umbrian tomato (Solanum lycopersicum L.) landraces through SSR markers and application for varietal identification. Genetic Resources and Crop Evolution 67(7): 1807-1820.

Cenci, A., Sardos, J., Hueber, Y., Martin, G., Breton, C., Roux, N., Swennen, R., Carpentier, S.C. & Rouard, M. 2021. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. Annals of Botany 127(1): 7-20.

Creste, S., Tulmann Neto, A., de Oliveira Silva, S. & Figueira, A. 2003. Genetic characterization of banana cultivars (Musa spp.) from Brazil using microsatellite markers. Euphytica 132: 259-268.

D’Hont, A., Denoeud, F., Aury, J.M., Baurens, F.C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., Alberti, A., Bernard, M., Correa, M., Ayyampalayam, S., McKain, M.R., Leebens-Mack, J., Burgess, D., Freeling, M., Mbéguié-A-Mbéguié, D., Chabannes, M., Wicker, T., Panaud, O., Barbosa, J., Hribova, E., Heslop-Harrison, P., Habas, R., Rivallan, R., Francois, P., Poiron, C., Kilian, A., Burthia, D., Jenny, C., Bakry, F., Brown, S., Guignon, V., Kema, G., Dita, M., Waalwijk, C., Joseph, S., Dievart, A., Jaillon, O., Leclercq, J., Argout, X., Lyons, E., Almeida, A., Jeridi, M., Dolezel, J., Roux, N., Risterucci, A.M., Weissenbach, J., Ruiz, M., Glaszmann, J.C., Quétier, F., Yahiaoui, N. & Wincker, P. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410): 213-217.

Doyle, J.J. & Doyle, J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12(1): 13-15.

Earl, D.A. & VonHoldt, B.M. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetic Resources 4: 359-361.

FAO. 2023. Banana Facts and Figures. https://www.fao.org/economic/est/est-commodities/oilcrops/bananas/bananafacts/en/#.YvMccXZBy72 Accessed July 13 2023.

Gemayel, R., Cho, J., Boeynaems, S. & Verstrepen, K.J. 2012. Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences. Genes 3(3): 461-480.

Hippolyte, I., Bakry, F., Seguin, M., Gardes, L., Rivallan, R., Risterucci, A.M., Jenny, C., Perrier, X., Carreel, F. & Argout, X. 2010. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas. BMC Plant Biology 10(1): 1-18.

Howell, E.C., Newbury, H.J., Swennen, R.L., Withers, L.A. & Ford-Lloyd, B.V. 1994. The use of RAPD for identifying and classifying Musa germplasm. Genome 37(2): 328-332.

Kim, M.J., Lee, Y.M., Suh, S.M. & Kim, H.Y. 2020. Species identification of red deer (Cervus elaphus), roe deer (Capreolus capreolus), and water deer (Hydropotes inermis) using capillary electrophoresis-based multiplex PCR. Foods 9(8): 982.

Martin, G., Cardi, C., Sarah, G., Ricci, S., Jenny, C., Fondi, E., Perrier, X., Glaszmann, J.C., D'Hont, A. & Yahiaoui, N. 2020. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana. The Plant Journal 102(5): 1008-1025.

Meng, Y.S., Zhao, N., Li, H., Zhai, H., He, S.Z. & Liu, Q.C. 2018. SSR fingerprinting of 203 sweetpotato (Ipomoea batatas (L.) Lam.) varieties. Journal of Integrative Agriculture 17(1): 86-93.

Nayar, M.N. 2010. The bananas: Botany, origin, dispersal. Horticultural Reviews 36(3): 117-164.

Nei, M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.

Ning, S.P., Xu, L.B., Lu, Y., Huang, B.Z. & Ge, X.J. 2007. Genome composition and genetic diversity of Musa germplasm from China revealed by PCR-RFLP and SSR markers. Scientia Horticulturae114(4): 281-288.

Peakall, R. & Smouse, P.E. 2006. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1): 288-295.

Perrier, X., De Langhe, E., Donohue, M., Lentfer, C., Vrydaghs, L., Bakry, F., Carreel, F., Hippolyte, I., Horry, J.P., Jenny, C., Lebot, V., Risterucci, A.M., Tomekpe, K., Doutrelepont, H., Ball, T., Manwaring, J., de Maret, P. & Denham, T. 2011. Multidisciplinary perspectives on banana (Musa spp.) domestication. Proceedings of the National Academy of Sciences 108(28): 11311-11318.

Perrier, X. & Jacquemoud-Collet, J.P. 2006. DARwin softwarehttp://darwin. cirad. fr/darwin

Prasad, M., Varshney, R. K., Roy, J., Balyan, H. & Gupta, P. 2000. The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theoretical Applied Genetics 100(3-4): 584.

Pritchard, J.K., Stephens, M. & Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959.

Pruvot-Woehl, S., Krishnan, S., Solano, W., Schilling, T., Toniutti, L., Bertrand, B. & Montagnon, C. 2020. Authentication of Coffea arabicavarieties through DNA fingerprinting and its significance for the coffee sector. Journal of AOAC INTERNATIONAL 103(2): 325-334.

Ravishankar, K.V., Vidhya, L., Cyriac, A., Rekha, A., Goel, R., Singh, N. & Sharma, T. 2012. Development of SSR markers based on a survey of genomic sequences and their molecular analysis in banana (Musa spp.). The Journal of Horticultural Science and Biotechnology 87(1): 84-88.

Rotchanapreeda, T., Wongniam, S., Swangpol, S.C., Chareonsap, P.P., Sukkaewmanee, N. & Somana, J. 2016. Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas. Plant Systematics and Evolution 302(7): 739-761.

Sánchez, E., Solano, W., Gatica-Arias, A., Chavarría, M. & Araya-Valverde, E. 2020. Microsatellite DNA fingerprinting of Coffea sp. germplasm conserved in Costa Rica through singleplex and multiplex PCR. Crop Breeding and Applied Biotechnology 20(1): e27812013.

Sardos, J., Perrier, X., Doležel, J., Hřibová, E., Christelová, P., Van Den Houwe, I., Kilian, A. & Roux, N. 2016. DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.). Annals of Botany 118(7): 1269-1278.

Simmonds, N.W. & Shepherd, K. 1955. The taxonomy and origins of the cultivated bananas. Botanical Journal of the Linnean Society 55(359): 302-312.

Spanoghe, M., Marique, T., Rivière, J., Lanterbecq, D. & Gadenne, M. 2015. Investigation and development of potato parentage analysis methods using multiplexed SSR fingerprinting. Potato Research 58: 43-65.

Suman, S. 2017. Plant tissue culture: A promising tool of quality material production with special reference to micropropagation of banana. Biochemical and Cellular Archives 17(1): 1-26.

Valmayor, R.V., Jamaluddin, S.H., Silayoi, B., Kusumo, S., Danh, L.D., Pascua, O.C. & Espino, R.R.C. 2000. Banana cultivar names and synonyms in Southeast Asia. In Advancing Banana and Plantain R&D in Asia and the Pacific, edited by Molina, A.B. & Roa, V.N. Proceeding of the 9th INIBAP-ASPNET Regional Advisory Committee held at South China Agricultural University, Guangzhou, China 2-5 November 1999,  pp. 55-66.

Verstrepen, K.J., Jansen, A., Lewitter, F. & Fink, G.R. 2005. Intragenic tandem repeats generate functional variability. Nature Genetics 37(9): 986-990.

Wang, X.L., Chiang, T.Y., Roux, N., Hao, G. & Ge, X.J. 2007. Genetic diversity of wild banana (Musa balbisiana Colla) in China as revealed by AFLP markers. Genetic Resources and Crop Evolution 54(5): 1125-1132.

Wang, Z., Miao, H., Liu, J., Xu, B., Yao, X., Xu, C., Zhao, S., Fang, X., Jia, C., Wang, J., Zhang, J., Li, J., Xu, Y., Wang, J., Ma, W., Wu, Z., Yu, L., Yang, Y., Liu, C., Guo, Y., Sun, S., Baurens, F. C., Martin, G., Salmon, F., Garsmeur, O., Yahiaoui, N., Hervouet, C., Rouard, M., Laboureau, N., Habas, R., Ricci, S., Peng, M., Guo, A., Xie, J., Li, Y., Ding, Z., Yan, Y., Tie, W., D’Hont, A., Hu, W. & Jin, Z. 2019. Musa balbisianagenome reveals subgenome evolution and functional divergence. Nature Plants 5(8): 810-821.

Ying, S.T. & Zaman, F.Q. 2006. DNA extraction from mature oil palm leaves. Journal of Oil Palm Research 18: 219.

 

*Pengarang untuk surat-menyurat; email: amer.iz@fgvholdings.com

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

   

sebelumnya