Study of genetic diversity and marker-trait association for sweetness by Target Region Amplification Polymorphism Polymerase Chain Reaction (TRAP-PCR) in Cucumis melo L.
Abstract
Cucumis melo (C. melo L.) groups is an important plant with increasing economic value. The improvement of the varieties with great tastes like melon and resistance to insect and unfavorable weather conditions similar to Thai-melon has been needed. This research aimed to study genetic diversity and relationship between molecular markers and sweetness trait of C. melo L. by using Target Region Amplified Polymorphism Polymerase Chain Reaction (TRAP-PCR) technique. Specific primers which were designed based on the sequence of nine genes involving in metabolic pathway of sugar combining with twelve arbitrary primers were used in TRAP-PCR. It was found that 59 pairs of primers were able to amplify DNA generating total 379 amplicons. The polymorphic data was used to create dendrogram based on Jaccard’s similarity index through UPGMA. The results revealed the similarity index ranged from 0.69 to 0.95. Studied plants could be divided into 3 groups with a similarity coefficient of 0.8, corresponding to the sweetness (% brix). The 220 of polymorphic bands were detected with a percentage of 58.05. Analysis of the relationship between molecular markers and sweetness trait showed thatCM01 (X174) marker was found to correlate with the sweetness of 87.07 percent, resulting from the use of primers, Neutral invertase 1 with Sa17_800. The results of genetic diversity and developed DNA markers in this study will assist breeding processes and selection of sweetness trait in C. melo L. to be more efficient, more accurate and faster. Keywords: Cucumis melo L., TRAP-PCR, Genetic diversity, Molecular marker, sweetnessReferences
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Alwala, S., Suman, Arro, J.A., Veremis, J.C., & Kimbeng, C.A. (2006). Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci, 46, 448-455.
Arro, J. A. (2005). Genetic diversity among sugarcane clones using target region amplification polymorphism (TRAP) markers and pedigree relationships. Retrieved January 12, 2018, from http://digitalcommons. lsu.edu/gradschool_theses/1094.
Burger, Y., Sa’ar, U., Distelfeld, A., Katzir, N., Yeselson, Y., Shen, S., & Schaffer, A.A. (2003). Development of sweet melon (Cucumis melon L.) genotypes combining high sucrose and organic acid content. J. Amer. Soc HORT. Sci,128, 537-540.
Chiewchanpanich, V. (1993). Varietal studies and yield trial of melon (Cucumis melo var. conomon). Retrieved June 15,2017, from http:// www.lib.kps.ku.ac.th/SpecialProject/Horticulture/2536/Bs/.../
WorranuchChAll.pdf. (in Thai)
Collard, B.C.Y. & Mackill, D.J., 2009, Start codon targeted (SCoT) polymorphism: A simple,novel DNA marker technique for generating gene-targeted markers in plants, Plant Mol. Biol. Rep, 27, 86-93.
Dai. N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z., Giovannoni, J., Burger, Y., Katzir, N., & Schaffer, A.A. (2011). Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol, 76, 1–18.
Garcia-Mas, J., Oliver, M., Gómez-Paniagua, H., & de Vicente, M.C. (2000). Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon. Theor Appl Genet, 101, 860-864.
Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M,. Mir, G., Gonzalez, V.M., Henaff, E., Camara, F., Cozzuto, L., Lowy, E., Alioto, T., Capella-Gutiérrez, S., Blanca, J., Canizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodríguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., Lorente-Galdos, B., Mele, M., Yang, L., Weng, Y., Navarr, A., Marques-Bonet, T., Aranda, M.A., Nuez, F., Pico, B., Gabaldon, T., Roma, G., Guigo, R., Casacuberta, J.M., Arus, P., & Puigdomènech, P. (2012). The genome of melon (Cucumis melo L.). PNAS, 29 (109), 11872 – 11877.
Hu, J., & Vick, B.A. (2003). Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol. Biol. Rep, 21, 289-294.
Hu, J., Ochoa, O.E., Truco, M.J., & Vick, B.A. (2005). Application of the TRAP technique to lettuce (Lactuca sativa L.) genotyping. Euphytica, 144, 225–235.
Hu, J. (2006). Defining the sunflower (Helianthus annuus L.) linkage group ends with the Arabidopsis-type telomere sequence repeat-derived markers. Chromosome Research, 14, 535–548.
Hwang, S.K., & Kim, Y. M. (2000). A simple and reliable method for preparation of cross-contamination free plant genome DNA for PCR-based detection of transgenes. Journal of biochemistry and molecular biology, 33, 537-546.
Inchonbot, S., Sakulsingharoj, C., Sangtong, V., Puddhanon, P., & Pongjaroenkit , S. (2015). Genetic diversity study of Cucumis melo L. by Random Amplification of Polymorphic DNA(RAPD) Technique. In Proceeding of 19th National Genetics Conference . (pp.314-319). Khonkaen University: kkuprinting. (in Thai)
Kacar, Y.A., Simsek, O., Solmaz, I., Sari, N., & Mendi, Y.Y. (2012). Genetic diversity among melon accessions (Cucumis melo) from Turkey based on SSR markers. Genet Mol Res, 11, 622–4631.
Khan, I.A., Bibi, S., Yasmeen, S., Seema, N., Khatri, A., Siddioui, M.A., Nizamani, G.S. & Afghan, S. 2011. Identification of elite sugarcane clones through TRAP. Pak. J. Bot., 43(1), 261-269.
Kohpayegani, J.A., & Behbahani, M. (2008). Genetic diversity of some populations of Iranian melon using SSR markers. Biotechnology, 7, 19-26.
Kong, Q., Gao, L., Cao, L., Liu, Y., Saba, H., Huang, Y., & Bie, Z. (2016). Assessment of suitable reference genes for quantitative gene expression studies in melon fruits. Plant science, 7, 1-10.
Kumar, Y., Kwon, S. J., Coyne, C. J., Hu, J., Kisha, T. J., Grusak, M. A., McGee, R. J., & Sarker, A. (2014). Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm. Genet Resour Crop Evol, 61, 965-977.
Li, G. & Quiros, C.F (2001). Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet, 103, 455–461.
Liu, Z.H., Anderson, J.A., Hu, J., Friesen, T.L., Rasmussen, J.B., & Faris, J.D. (2005). A wheat intervarietal linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor. Appl. Gene, 111, 782–794.
Miklas, P.N., Kelly, J.D., Beebe, S.E., & Blair, M.W. (2006). Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding, Euphytica 147, 105-131.
Miklas, P.N., Hu, J., Grunwald, N.J., & Larsen, K.M. (2006). Potential application of TRAP markers for tagging disease resistance traits in common bean. Crop Sci, 46, 910-916.
Mukunda Lakshmi, L., Mohan Rao A. Ramesh, A., & Lingaiah, H.B. (2017). RAPD Molecular Marker Based Genetic Diversity among Oriental Pickling Melon (Cucumis melo var. conomon) Genotypes in Karnataka, India. International Journal of Current Microbiology and Applied Science, 6(3), 324-330.
Niramit Kitroongruang. 1988. A study of F1 Hybrid Characters of Muskmelo (Cucumis melo L.) .Thesis.
Chiang Mai University.
Niyompanich, S., Binchai. S., Pringsulaka, O., & Rangsiruji, A. (2017). Clustering and Genetic Divesity Assessment of Economic Cultivars of Melons (Cucumis melo L.) Using Molecular Techniques. Srinakharinwirot University Science Journal, 33(2), 71-87. (in Thai)
Palumbo, R., Hong, W.F., Wang, G.L., Hu, J., Craig, R., Locke, J., Krause, C., & Tay, D. (2007). Target region amplification polymorphism (TRAP) as a tool for detecting genetic variation in the genus pelargonium. Hortscience, 42(5), 1118-1123.
Qiu, C., Wenjuan, Y., Wangqiu, D., Bin, S., & Taihui, L. (2014). Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism. The Scientific World Journal, 2014, 1-7.
Saladie, M., Canizares, J., Phillips, M.A., Rodriguez-Concepcion, M., Larrigaudiere, C., Gibon, Y., Stitt, M., Lunn, J.E., & Garcia-Mas, J. (2015). Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics, 16, 440 (1-20).
Sheng, Y., Luan, F., Chen, K., Cui, X., & Staub, J.E. (2007). Genetic diversity of chinese thin-skinned melon cultivars (Cucumis melo L.) Based on simple sequence repeat markers. Acta Hort, 763, 169-176.
Souza, P.A., Adriano Nascimento Simões, A.N., Puiatti, M., Gomes, J., & Vieira, M.R. (2013). Carbohydrate metabolism and quality of fruits from the Cucumis genus. Academia Journal of Agricultural Research, 1(7), 101-105.
Suman, A., Ali, K., Arro, J., Arnold, S., Parco, A.S., Kimbeng, C. A., & Baisakh, N. (2012). Molecular diversity among members of the Saccharum complex assessed using TRAP markers based on lignin-related genes. Bioenerg.Res, 5, 197-205.
Tira-umphon, A., & Ketudat-Cairns, M. (2015). Genetic Variation and Morphological Traits in Melon and Pickling Melon from ISSR. Retrieved Mach 18, 2017, from http://www.sutir.sut.ac.th.8080/sutir/ bitstream/ 123456789/5894/1/Fulltext.pdf (in Thai)
Xiao, Y., Liu, W., Lu, Y.Y., Gong, W.B., & Bian, Y.B. (2010). Applying target region amplification polymorphism markers for analyzing genetic diversity of Lentinula edodes in China. Journal of Basic Microbiology,
50, 1-9.
Zhang, H., Wang, H., Yi, H., Zhai, W., Wang, G., & Fu, Q. (2016). Transcriptome profiling of Cucucmis melo fruit development and ripening. Horticulture Research, 3, 16014.
Alwala, S., Suman, Arro, J.A., Veremis, J.C., & Kimbeng, C.A. (2006). Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci, 46, 448-455.
Arro, J. A. (2005). Genetic diversity among sugarcane clones using target region amplification polymorphism (TRAP) markers and pedigree relationships. Retrieved January 12, 2018, from http://digitalcommons. lsu.edu/gradschool_theses/1094.
Burger, Y., Sa’ar, U., Distelfeld, A., Katzir, N., Yeselson, Y., Shen, S., & Schaffer, A.A. (2003). Development of sweet melon (Cucumis melon L.) genotypes combining high sucrose and organic acid content. J. Amer. Soc HORT. Sci,128, 537-540.
Chiewchanpanich, V. (1993). Varietal studies and yield trial of melon (Cucumis melo var. conomon). Retrieved June 15,2017, from http:// www.lib.kps.ku.ac.th/SpecialProject/Horticulture/2536/Bs/.../
WorranuchChAll.pdf. (in Thai)
Collard, B.C.Y. & Mackill, D.J., 2009, Start codon targeted (SCoT) polymorphism: A simple,novel DNA marker technique for generating gene-targeted markers in plants, Plant Mol. Biol. Rep, 27, 86-93.
Dai. N., Cohen, S., Portnoy, V., Tzuri, G., Harel-Beja, R., Pompan-Lotan, M., Carmi, N., Zhang, G., Diber, A., Pollock, S., Karchi, H., Yeselson, Y., Petreikov, M., Shen, S., Sahar, U., Hovav, R., Lewinsohn, E., Tadmor, Y., Granot, D., Ophir, R., Sherman, A., Fei, Z., Giovannoni, J., Burger, Y., Katzir, N., & Schaffer, A.A. (2011). Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol, 76, 1–18.
Garcia-Mas, J., Oliver, M., Gómez-Paniagua, H., & de Vicente, M.C. (2000). Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon. Theor Appl Genet, 101, 860-864.
Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M,. Mir, G., Gonzalez, V.M., Henaff, E., Camara, F., Cozzuto, L., Lowy, E., Alioto, T., Capella-Gutiérrez, S., Blanca, J., Canizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodríguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., Lorente-Galdos, B., Mele, M., Yang, L., Weng, Y., Navarr, A., Marques-Bonet, T., Aranda, M.A., Nuez, F., Pico, B., Gabaldon, T., Roma, G., Guigo, R., Casacuberta, J.M., Arus, P., & Puigdomènech, P. (2012). The genome of melon (Cucumis melo L.). PNAS, 29 (109), 11872 – 11877.
Hu, J., & Vick, B.A. (2003). Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol. Biol. Rep, 21, 289-294.
Hu, J., Ochoa, O.E., Truco, M.J., & Vick, B.A. (2005). Application of the TRAP technique to lettuce (Lactuca sativa L.) genotyping. Euphytica, 144, 225–235.
Hu, J. (2006). Defining the sunflower (Helianthus annuus L.) linkage group ends with the Arabidopsis-type telomere sequence repeat-derived markers. Chromosome Research, 14, 535–548.
Hwang, S.K., & Kim, Y. M. (2000). A simple and reliable method for preparation of cross-contamination free plant genome DNA for PCR-based detection of transgenes. Journal of biochemistry and molecular biology, 33, 537-546.
Inchonbot, S., Sakulsingharoj, C., Sangtong, V., Puddhanon, P., & Pongjaroenkit , S. (2015). Genetic diversity study of Cucumis melo L. by Random Amplification of Polymorphic DNA(RAPD) Technique. In Proceeding of 19th National Genetics Conference . (pp.314-319). Khonkaen University: kkuprinting. (in Thai)
Kacar, Y.A., Simsek, O., Solmaz, I., Sari, N., & Mendi, Y.Y. (2012). Genetic diversity among melon accessions (Cucumis melo) from Turkey based on SSR markers. Genet Mol Res, 11, 622–4631.
Khan, I.A., Bibi, S., Yasmeen, S., Seema, N., Khatri, A., Siddioui, M.A., Nizamani, G.S. & Afghan, S. 2011. Identification of elite sugarcane clones through TRAP. Pak. J. Bot., 43(1), 261-269.
Kohpayegani, J.A., & Behbahani, M. (2008). Genetic diversity of some populations of Iranian melon using SSR markers. Biotechnology, 7, 19-26.
Kong, Q., Gao, L., Cao, L., Liu, Y., Saba, H., Huang, Y., & Bie, Z. (2016). Assessment of suitable reference genes for quantitative gene expression studies in melon fruits. Plant science, 7, 1-10.
Kumar, Y., Kwon, S. J., Coyne, C. J., Hu, J., Kisha, T. J., Grusak, M. A., McGee, R. J., & Sarker, A. (2014). Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm. Genet Resour Crop Evol, 61, 965-977.
Li, G. & Quiros, C.F (2001). Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet, 103, 455–461.
Liu, Z.H., Anderson, J.A., Hu, J., Friesen, T.L., Rasmussen, J.B., & Faris, J.D. (2005). A wheat intervarietal linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor. Appl. Gene, 111, 782–794.
Miklas, P.N., Kelly, J.D., Beebe, S.E., & Blair, M.W. (2006). Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding, Euphytica 147, 105-131.
Miklas, P.N., Hu, J., Grunwald, N.J., & Larsen, K.M. (2006). Potential application of TRAP markers for tagging disease resistance traits in common bean. Crop Sci, 46, 910-916.
Mukunda Lakshmi, L., Mohan Rao A. Ramesh, A., & Lingaiah, H.B. (2017). RAPD Molecular Marker Based Genetic Diversity among Oriental Pickling Melon (Cucumis melo var. conomon) Genotypes in Karnataka, India. International Journal of Current Microbiology and Applied Science, 6(3), 324-330.
Niramit Kitroongruang. 1988. A study of F1 Hybrid Characters of Muskmelo (Cucumis melo L.) .Thesis.
Chiang Mai University.
Niyompanich, S., Binchai. S., Pringsulaka, O., & Rangsiruji, A. (2017). Clustering and Genetic Divesity Assessment of Economic Cultivars of Melons (Cucumis melo L.) Using Molecular Techniques. Srinakharinwirot University Science Journal, 33(2), 71-87. (in Thai)
Palumbo, R., Hong, W.F., Wang, G.L., Hu, J., Craig, R., Locke, J., Krause, C., & Tay, D. (2007). Target region amplification polymorphism (TRAP) as a tool for detecting genetic variation in the genus pelargonium. Hortscience, 42(5), 1118-1123.
Qiu, C., Wenjuan, Y., Wangqiu, D., Bin, S., & Taihui, L. (2014). Genetic diversity analysis of Hypsizygus marmoreus with target region amplification polymorphism. The Scientific World Journal, 2014, 1-7.
Saladie, M., Canizares, J., Phillips, M.A., Rodriguez-Concepcion, M., Larrigaudiere, C., Gibon, Y., Stitt, M., Lunn, J.E., & Garcia-Mas, J. (2015). Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. BMC Genomics, 16, 440 (1-20).
Sheng, Y., Luan, F., Chen, K., Cui, X., & Staub, J.E. (2007). Genetic diversity of chinese thin-skinned melon cultivars (Cucumis melo L.) Based on simple sequence repeat markers. Acta Hort, 763, 169-176.
Souza, P.A., Adriano Nascimento Simões, A.N., Puiatti, M., Gomes, J., & Vieira, M.R. (2013). Carbohydrate metabolism and quality of fruits from the Cucumis genus. Academia Journal of Agricultural Research, 1(7), 101-105.
Suman, A., Ali, K., Arro, J., Arnold, S., Parco, A.S., Kimbeng, C. A., & Baisakh, N. (2012). Molecular diversity among members of the Saccharum complex assessed using TRAP markers based on lignin-related genes. Bioenerg.Res, 5, 197-205.
Tira-umphon, A., & Ketudat-Cairns, M. (2015). Genetic Variation and Morphological Traits in Melon and Pickling Melon from ISSR. Retrieved Mach 18, 2017, from http://www.sutir.sut.ac.th.8080/sutir/ bitstream/ 123456789/5894/1/Fulltext.pdf (in Thai)
Xiao, Y., Liu, W., Lu, Y.Y., Gong, W.B., & Bian, Y.B. (2010). Applying target region amplification polymorphism markers for analyzing genetic diversity of Lentinula edodes in China. Journal of Basic Microbiology,
50, 1-9.
Zhang, H., Wang, H., Yi, H., Zhai, W., Wang, G., & Fu, Q. (2016). Transcriptome profiling of Cucucmis melo fruit development and ripening. Horticulture Research, 3, 16014.
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2018-05-31
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