Genome evaluation of banana cultivars based on morphological character and Inter-Simple Sequence Repeat (ISSR) molecular marker
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Abstract. 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. This study aims to evaluate the genome group and to investigate the genetic variability of banana cultivar using morphological character and ISSR molecular marker. Fourteen banana cultivars with genomic group AA, AAA, AAB, ABB, and BB was used. All samples were Identified morphologically based on minimal descriptors for bananas issued by the International Plant Genetic Resources Institute (IPGRI). Total genomic DNA was extracted using DNA Isolation Kit Promega Wizard®. ISSR primer was used in this study, including UBC834, UBC835, UBC843, UBC848, and UBC855. Clustering analysis was used to evaluate genome grouping of the banana cultivar. Clustering analysis of morphological character was performed using the unweighted pair group method with arithmetic mean (UPGMA) algorithm and Bray-Curtis coefficient similarity using Paleontological Statistics (PAST) software. Morphological and ISSR was successfully differentiate banana cultivars and relatively similar to previous genome grouping. However, pisang Triolin (AAB) must be evaluated since it belongs to AAA group. The identification of cultivars and classification of their genome groups based on morphological characteristics and proved by molecular markers will strengthen the establishment of Musa improvement strategy especially in Indonesia and ease the breeder to identify desirable traits of progenitor to be included in the breeding program.
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References
Ahmad F, Megia R, Poerba YS. 2014. Genetic diversity of Musa balbisiana Colla in Indonesia based on AFLP marker. HAYATI Journal of Biosciences 21(1): 39-47.
Atom, Devi A, Lalrinfela P, Robert Thangjam. 2015. Genome classification of banana genetic resources of Manipur using morphological characters. Science Vision 15 (4), 189-195.
Babu AG, Prabhuling G, Rashmi S Karani, Satish D, Patil RK, Mulla SR, Raghavendra G, Jagadeesha RC. 2018. Genetic diversity analysis among banana cultivars through ISSR markers. J Pharmacog and Phytochem 7(6): 1576-1580.
Dhakshanamoorthy D, Selvaraj R, Chidambaramb A. 2014. Utility of RAPD marker for genetic diversity analysis in gamma-rays and ethyl methane sulphonate (EMS)-treated Jatropha curcas plants. CR Biol 338, 75-82.
Das, Chandra S, Balamohan TN, Poornima K, Bergh IVD. 2018. Evaluation of Genetic Diversity in Some Banana Hybrids using ISSR Markers. Int J Curr Microbiol App Sci 7(1): 146-157.
Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. 2013. A draft Musa balbisiana genome sequence for molecular genetics in ploidy, inter- and intraspecific Musa hybrids. BMC Genomics 14: 683.
De Langhe ED, Vrydaghs EL, de Maret P, Perrier X, Denham T. 2009. Why bananas matter: An introduction to the history of banana domestication. Ethnobotany Res Appl 7:165-177.
Frison EA, Escalant JV, Sharrock S. 2004. The global Musa genomic consortium: A boost for banana improvement. In: Jain SM, Swennen R (eds) Banana improvement: Cellular, molecular biology, and induced mutations. Science Publishers, Enfield.
Garcia SAL, Talebi R, Ferreira CF, Vroh BI, Paiva LV, Kema GHJ, Souza MT. 2011. Identification and validation of est-derived molecular markers, TRAP and VNTRS, for banana research. Acta Hort 897: 69-80.
Gusmiati LH, Hapsari L, Wahyudi D. 2018. Morphological diversity and clustering of 10 cooking bananas (Musa cv. Group ABB) collection of Purwodadi Botanic Garden – LIPI. Floribunda 5(8): 299–314. [Indonesian]
Hapsari L. 2014. Wild Musa species collection of Purwodadi Botanic Garden: inventory and its morpho-taxonomic review. The Journal of Tropical Life Science 4(1): 70-80. [Indonesian]
Hapsari L, Wahyudi D, Azrianingsih R, Arumingtyas EL. 2015. Genome identification of bananas (Musa spp.) from East Java assessed with PCR-RFLP of the Internal Transcribed Spacer ribosomal DNA. Int J Biosci 7(3): 42-52.
Hapsari L, Lestari DA. 2016. Fruit characteristic and nutrient values of four Indonesian banana cultivars (Musa spp.) at different genomic groups. J Sci 38(3): 303-311.
Hapsari L, Kennedy J, Lestari DA, Masrum A, Lestarini W. 2017. Ethnobotanical survey of bananas (Musaceae) in six districts of East Java, Indonesia. Biodiversitas. 18(1), 160-174.
Heslop-Harrison JS, Schwarzacher T. 2007. Domestication, genomics and the future for banana. Ann Bot 100:1073–1084.
International Plant Genetic Resources Institute (IPGRI). 1996. Descriptor for Banana (Musa spp). Montpellier, Perancis.
Kharadi, Ankit, Chaudhary S, Pandey M, Chaudhary A, Sharma MC, Chikara SK. 2014. Analysis of genetic diversity amongst banana cultivars prevalent in gujarat region of india using ISSR markers. Indian J Biotech Pharm Res 2(2):14-20.
Kumakech A, Kiggundu A, Okori P. 2013. Reaction of Musa balbisiana to banana bacterial wilt infection. Afr Crop Sci J 21:337-346.
Laurentin H and Karlovsky P. 2007. AFLP ?ngerprinting of sesame (Sesamum indicum L.) cultivars: identi?cation, genetic relationship and comparison of AFLP informativeness parameters. Genet Resour Crop Evol 54: 1437–1446.
Nasution RE. 1991. A taxonomic study of the species Musa acuminata Colla with ITS intraspecific taxa in Indonesia. Memoirs of Tokyo University of Agriculture 32: 1-122.
Nikmah IA, Azrianingsih R, Wahyudi D. 2016. Genetic diversity of porang populations (Amorphophallus muelleri Blume) in Central Java and West Java based on LEAFY second intron marker. The Journal of Tropical Life Science 6: 23-27. [Indonesian]
Nwakanma DC, Pillay M, Okoli BE, Tenkouano A. 2003. PCR-RFLP of the ribosomal DNA internal transcribed spacers (ITS) provides markers for the A and B genomes in Musa L. Theor Appl Genet 108: 154–159.
Nybom H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13(5):1143-55.
Oliveira MAP, Valls JFM. 2003. Morphological characterization and reproductive aspects in genetic variability studies of forage peanut. Sci Agric 60: 299-304.
Padmesh P, S. Mukunthakumar S,. Vineesh PS, Skaria R, Kumar KH, Krishnan PN. 2012. Exploring wild genetic resources of Musa acuminata Colla distributed in the humid forests of southern Western Ghats of peninsular India using ISSR markers. Plant Cell Rep 31: 1591-1601.
Perrier X, Langhe ED, Donohue M, Lentfer C, Vrydaghs L, Bakry F, Carreel F, Hippolyite I, Horry J-P, Jenny C, lebot V, Risterucci A-M, Tomekpe K, Doutrelepont H, Ball T, Manwaring J, Maret PD, Denham T. 2011. Multidisciplinary perspectives on banana (Musa spp.) domestication. PNAS 108(28):113-118.
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.
Poerba YS, Martanti D, Ahmad F. 2018. Genetic variation of wild Musa acuminata Colla from Indonesia based on RAPD and ISSR markers. Biotropia 26(2): 1-18. [Indonesian]
Probojati RT, Wahyudi D, Hapsari L. 2019. Clustering analysis and genome inference of Pisang Raja local cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. Journal of Tropical Biodiversity and Biotechnology 4(2): 42 - 53. [Indonesian]
Ray T, Dutta I, Saha P, Das S, Roy SC. 2006. Genetic stability of three economically important micropropagated banana (Musa spp.) cultivars of lower Indo-Gangetic plains, as assessed by RAPD and ISSR markers. Plant Cell Tiss Org Cult 2006; 85 (1) 11–21.
Singh N, Ashish K. Pal, Meena B, Roy RK, Tamta S, Rana TS. 2017. Development of ISSR- and RAPD-derived SCAR markers for identification of Gladiolus germplasm. J Hortic Sci Biotech 92: 577-582.
Simmonds NW, Shepherd K. 1955. The taxonomy and origins of cultivated bananas. Bot Linnean Society. Botanical J. 55:302–312
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R, Wahyudi D. 2017. Genetic variability of local durian (Durio zibethinus Murr.) in Ternate Island based on rapd markers. Plant Cell Biotechnol Molecul Biol 18: 68-75.
Sumardi I, Wulandari M. 2010. Anatomy and morphology character of five Indonesian banana cultivars (Musa spp.) of different ploidy level. Biodiversitas. 11(4): 167-175.
Vanhove AC, Vermaelen W, Panis B, Swennen R, Carpentier SC. 2012. Screening the banana biodiversity for drought tolerance: can an in vitro growth model and proteomics be used as a tool to discover tolerant varieties and understand homeostasis. Front Plant Sci 3:176.
Valdez-Ojeda R, James-Kay A, Ku-Cauich J, Escobedo-Gracia Medrano RM. 2014. Genetic relationships among a collection of Musa germplasm by fluorescent-labelled SRAP. Tree Genet Genomes 10(3): 465-476.
Valmayor RV, Jamaluddin SH, Silayoni B, Kusumo S, Danh LD, Pascua OC, Espino RRC. 2000. Banana Cultivar names and synonims in south asia. INIBAP, Los Banos Philipines.
Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A. 2007. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173: 638–649.
Wahyudi D, Azrianingsih R, Mastuti R. 2015. Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences. Journal of Biodiversity and Environmental Sciences 3: 31-41.
Youssef M, James A, Rivera-Madrid R, Ortiz R, Escobedo-Gracia Medrano RM. 2011. Musa genetic diversity revealed by SRAP and AFLP. Mol Biotech 47(3): 189–199.
Atom, Devi A, Lalrinfela P, Robert Thangjam. 2015. Genome classification of banana genetic resources of Manipur using morphological characters. Science Vision 15 (4), 189-195.
Babu AG, Prabhuling G, Rashmi S Karani, Satish D, Patil RK, Mulla SR, Raghavendra G, Jagadeesha RC. 2018. Genetic diversity analysis among banana cultivars through ISSR markers. J Pharmacog and Phytochem 7(6): 1576-1580.
Dhakshanamoorthy D, Selvaraj R, Chidambaramb A. 2014. Utility of RAPD marker for genetic diversity analysis in gamma-rays and ethyl methane sulphonate (EMS)-treated Jatropha curcas plants. CR Biol 338, 75-82.
Das, Chandra S, Balamohan TN, Poornima K, Bergh IVD. 2018. Evaluation of Genetic Diversity in Some Banana Hybrids using ISSR Markers. Int J Curr Microbiol App Sci 7(1): 146-157.
Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. 2013. A draft Musa balbisiana genome sequence for molecular genetics in ploidy, inter- and intraspecific Musa hybrids. BMC Genomics 14: 683.
De Langhe ED, Vrydaghs EL, de Maret P, Perrier X, Denham T. 2009. Why bananas matter: An introduction to the history of banana domestication. Ethnobotany Res Appl 7:165-177.
Frison EA, Escalant JV, Sharrock S. 2004. The global Musa genomic consortium: A boost for banana improvement. In: Jain SM, Swennen R (eds) Banana improvement: Cellular, molecular biology, and induced mutations. Science Publishers, Enfield.
Garcia SAL, Talebi R, Ferreira CF, Vroh BI, Paiva LV, Kema GHJ, Souza MT. 2011. Identification and validation of est-derived molecular markers, TRAP and VNTRS, for banana research. Acta Hort 897: 69-80.
Gusmiati LH, Hapsari L, Wahyudi D. 2018. Morphological diversity and clustering of 10 cooking bananas (Musa cv. Group ABB) collection of Purwodadi Botanic Garden – LIPI. Floribunda 5(8): 299–314. [Indonesian]
Hapsari L. 2014. Wild Musa species collection of Purwodadi Botanic Garden: inventory and its morpho-taxonomic review. The Journal of Tropical Life Science 4(1): 70-80. [Indonesian]
Hapsari L, Wahyudi D, Azrianingsih R, Arumingtyas EL. 2015. Genome identification of bananas (Musa spp.) from East Java assessed with PCR-RFLP of the Internal Transcribed Spacer ribosomal DNA. Int J Biosci 7(3): 42-52.
Hapsari L, Lestari DA. 2016. Fruit characteristic and nutrient values of four Indonesian banana cultivars (Musa spp.) at different genomic groups. J Sci 38(3): 303-311.
Hapsari L, Kennedy J, Lestari DA, Masrum A, Lestarini W. 2017. Ethnobotanical survey of bananas (Musaceae) in six districts of East Java, Indonesia. Biodiversitas. 18(1), 160-174.
Heslop-Harrison JS, Schwarzacher T. 2007. Domestication, genomics and the future for banana. Ann Bot 100:1073–1084.
International Plant Genetic Resources Institute (IPGRI). 1996. Descriptor for Banana (Musa spp). Montpellier, Perancis.
Kharadi, Ankit, Chaudhary S, Pandey M, Chaudhary A, Sharma MC, Chikara SK. 2014. Analysis of genetic diversity amongst banana cultivars prevalent in gujarat region of india using ISSR markers. Indian J Biotech Pharm Res 2(2):14-20.
Kumakech A, Kiggundu A, Okori P. 2013. Reaction of Musa balbisiana to banana bacterial wilt infection. Afr Crop Sci J 21:337-346.
Laurentin H and Karlovsky P. 2007. AFLP ?ngerprinting of sesame (Sesamum indicum L.) cultivars: identi?cation, genetic relationship and comparison of AFLP informativeness parameters. Genet Resour Crop Evol 54: 1437–1446.
Nasution RE. 1991. A taxonomic study of the species Musa acuminata Colla with ITS intraspecific taxa in Indonesia. Memoirs of Tokyo University of Agriculture 32: 1-122.
Nikmah IA, Azrianingsih R, Wahyudi D. 2016. Genetic diversity of porang populations (Amorphophallus muelleri Blume) in Central Java and West Java based on LEAFY second intron marker. The Journal of Tropical Life Science 6: 23-27. [Indonesian]
Nwakanma DC, Pillay M, Okoli BE, Tenkouano A. 2003. PCR-RFLP of the ribosomal DNA internal transcribed spacers (ITS) provides markers for the A and B genomes in Musa L. Theor Appl Genet 108: 154–159.
Nybom H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13(5):1143-55.
Oliveira MAP, Valls JFM. 2003. Morphological characterization and reproductive aspects in genetic variability studies of forage peanut. Sci Agric 60: 299-304.
Padmesh P, S. Mukunthakumar S,. Vineesh PS, Skaria R, Kumar KH, Krishnan PN. 2012. Exploring wild genetic resources of Musa acuminata Colla distributed in the humid forests of southern Western Ghats of peninsular India using ISSR markers. Plant Cell Rep 31: 1591-1601.
Perrier X, Langhe ED, Donohue M, Lentfer C, Vrydaghs L, Bakry F, Carreel F, Hippolyite I, Horry J-P, Jenny C, lebot V, Risterucci A-M, Tomekpe K, Doutrelepont H, Ball T, Manwaring J, Maret PD, Denham T. 2011. Multidisciplinary perspectives on banana (Musa spp.) domestication. PNAS 108(28):113-118.
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.
Poerba YS, Martanti D, Ahmad F. 2018. Genetic variation of wild Musa acuminata Colla from Indonesia based on RAPD and ISSR markers. Biotropia 26(2): 1-18. [Indonesian]
Probojati RT, Wahyudi D, Hapsari L. 2019. Clustering analysis and genome inference of Pisang Raja local cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. Journal of Tropical Biodiversity and Biotechnology 4(2): 42 - 53. [Indonesian]
Ray T, Dutta I, Saha P, Das S, Roy SC. 2006. Genetic stability of three economically important micropropagated banana (Musa spp.) cultivars of lower Indo-Gangetic plains, as assessed by RAPD and ISSR markers. Plant Cell Tiss Org Cult 2006; 85 (1) 11–21.
Singh N, Ashish K. Pal, Meena B, Roy RK, Tamta S, Rana TS. 2017. Development of ISSR- and RAPD-derived SCAR markers for identification of Gladiolus germplasm. J Hortic Sci Biotech 92: 577-582.
Simmonds NW, Shepherd K. 1955. The taxonomy and origins of cultivated bananas. Bot Linnean Society. Botanical J. 55:302–312
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R, Wahyudi D. 2017. Genetic variability of local durian (Durio zibethinus Murr.) in Ternate Island based on rapd markers. Plant Cell Biotechnol Molecul Biol 18: 68-75.
Sumardi I, Wulandari M. 2010. Anatomy and morphology character of five Indonesian banana cultivars (Musa spp.) of different ploidy level. Biodiversitas. 11(4): 167-175.
Vanhove AC, Vermaelen W, Panis B, Swennen R, Carpentier SC. 2012. Screening the banana biodiversity for drought tolerance: can an in vitro growth model and proteomics be used as a tool to discover tolerant varieties and understand homeostasis. Front Plant Sci 3:176.
Valdez-Ojeda R, James-Kay A, Ku-Cauich J, Escobedo-Gracia Medrano RM. 2014. Genetic relationships among a collection of Musa germplasm by fluorescent-labelled SRAP. Tree Genet Genomes 10(3): 465-476.
Valmayor RV, Jamaluddin SH, Silayoni B, Kusumo S, Danh LD, Pascua OC, Espino RRC. 2000. Banana Cultivar names and synonims in south asia. INIBAP, Los Banos Philipines.
Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A. 2007. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173: 638–649.
Wahyudi D, Azrianingsih R, Mastuti R. 2015. Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences. Journal of Biodiversity and Environmental Sciences 3: 31-41.
Youssef M, James A, Rivera-Madrid R, Ortiz R, Escobedo-Gracia Medrano RM. 2011. Musa genetic diversity revealed by SRAP and AFLP. Mol Biotech 47(3): 189–199.
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