Assessment of Genetic Diversity based on RAPD Analysis in Cultivars of Peppers (Capsicum annuum, Capsicum chinense and Capsicum frutescens) Grown in Nigeria
Keywords:
Capsicum, genetic diversity, germplasm conservation, RAPD markers, unique allele
Abstract
Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity among 24 Capsicum cultivars collected from some states in Nigeria. These cultivars differ in their fruit morphology. 18 RAPD markers detected a total of 176 alleles (mean, 9.78; range, 515). Unique alleles (22) were found in 10 Capsicum cultivars. Genetic distance based on Jaccard coefficient range from 0.21 to 0.88, with an average of 0.61. Line pairs in Capsicum annuum (rodo) ranged from 0.21 to 0.63. A dendrogram based on RAPD markers divided the lines into 4 main groups and 1 line, which separated from other lines. The first group included 9 CR lines (Capsicum annuum) while the second group included 7 CS lines (Capsicum frutescens). The third group contained 1 CT (Capsicum annuum) and 2 CA lines (Capsicum frutescens). Lastly, the fourth group was separated into 2 subgroups; the first subgroup included the closely related cultivars CG (CG22 and CG23) lines (Capsicum annuum) whereas the second subgroup included CS17 and CA21 (Capsicum frutescens).
Principal component analysis (PCA) also grouped the lines and these were consistent with the dendrogram groupings. The grouping of these lines reflected their genetic similarity at the species level. These results define the existence of genetic diversity in the Capsicum species grown in some Nigerian states, which might be useful for future decisions in their conservation and management strategies.
References
Adetula, O. A. (2006). Genetic diversity of Capsicum using random amplified polymorphic DNAs. Afr. J. Biotechnol. 5: 120–122.
Ado, S. G. (1990). Pepper Production Guide: Extension Publication Submitted to the Horticultural Crops Research Programme. I. A. R. Samaru, p. 12.
Aguilar-Meléndez, A., Morrell, P. L., Roose, M. L. and Kim S.-C. (2009). Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am. J. Bot. 96(6): 1190–1202.
Bosland, P. W. and Votava, E. (1999). Peppers: Vegetable and Spices Capsicums. Oxford, UK: CABI Publishing. 204pp.
Baral, J. and Bosland, P. W. (2002). Genetic diversity of a Capsicum germplasm collection from Nepal as determined by Randomly Amplified Polymorphic DNA markers. J. Amer. Soc. Hort. Sci. 127(3): 316–324.
Buckler, E. S., Thornsberry, J. M. and Kresovich, S. (2001). Molecular diversity, structure and domestication of grasses. Genet. Res. 77: 213–218.
Dellaporta, S. L., Wood, J. and Hicks, J. B. (1983). “A plant DNA mini-preparation: version II. Plant Mol. Biol. Rep. 1(4): 19–21.
DeWitt, D. and Bosland, P. W. (1993). The pepper garden. Berkeley, California, Ten Speed Press. 209pp.
Djian-Caporalino, C., Lefebvre, V., Sage-Daubčze, A. M. and Palloix, A. (2007). Capsicum. In: Singh, R. J. and Jauhar, P. P. (eds.) Genetic resources, chromosome engineering and crop improvement. Vol. 3. Vegetable crops. CRC Press/Taylor and Francis Group, Boca Raton, p. 186–245.
Doebley, J. F., Gau, B. S. and Smith, B. D. (2006). The molecular genetics of crop domestication. Cell. 127: 1309–1321.
Erinle, I. D. (1989). Present status and prospects for?
increased production of tomato and pepper in Nigeria. In AVEDC Ed. Proc. Inter. I Sympt. Integrated Management Practices. p. 536–547.
González-Pérez, S., Garcés-Claver, A., Mallor, C., Sáenz de Miera, L. E., Fayos, O. Pomar, F. Merino, F and Silvar. C. (2014). New Insights into Capsicum spp Relatedness and the Diversification Process of C. annuum in Spain. 9(12): e116276.
Guzmán, F. A., Ayala, H., Azurdia, C., Duque, M. C., de Vicente, M. C. (2005). AFLP assessment of genetic diversity of Capsicum genetic resources in Guatemala: Home gardens as an option for conservation. Crop Sci. 45: 363–370.
Hernández-Verdugo, S., Luna-Reyes, R. and Oyama, K. (2001). Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Syst. Evol. 226(3): 129–142.
Hill, T. A., Ashra?, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M. J., Kozik, A., Michelmore, R. W., Van Deynze, A. (2013). Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip. PLoS One 8(2): e56200.
Lanteri, S., Acquadro, A. Quagliotti, L. and Portis. E. (2003). RAPD and AFLP assessment of genetic variation in a landrace of pepper (Capsicum annuum L.), grown in North-West Italy. Genet. Resour. Crop Ev. 50(7): 723–735.
Lee, J. M., Nahm, S. H., Kim, Y. M., Kim, B. D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor. Appl. Genet. 108: 619–627.
Odeigah, P. G. C., Oboh, B. and Aghalokpe, I. O. (1999). The characterization of Nigerian varieties of pepper, Capsicum annuum and Capsicum frutescens by SDS-polyacryl amide gel electrophoresis of seed proteins. Genet. Resour. Crop Ev. 46(2): 127–131.
Paran, I., Aftergoot, E. and Shifriss. C. (1998). Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica. 99(3): 167–173.
Pacheco-Olvera, A., Hernández-Verdugo, S., Rocha-Ramírez, V., González-Rodríguez, A. and Oyama, K. (2012). Genetic diversity and structure of pepper (Capsicum annuum L.) from NW Mexico analyzed by micro-satellite markers. Crop Sci. 52: 231–241.
Pickersgill B. (1997). Genetic resources and breeding of Capsicum spp. Euphytica. 96: 129–133.
Prince, J. P., Loaiza-Figueroa, F. and Tanksley, S. D. (1992). Restriction fragment length poly-morphism and genetic distance among Mexican accessions of Capsicum. Genome. 35: 726–732.
Rodriguez, J. M., Berke, T., Engle, L. and Nienhuis, J. (1999). Variation among and within Capsicum species revealed by RAPD markers. Theor. Appl. Genet. 99: 147–156.
Sneath, P. H. A. and Sokal, R. R. (1973). Numerical taxonomy. Freeman, San Francisco, CA, USA. 573pp.
Stágel, A., Gyurjan, I., Sasvari, Z., Lanteri, S., Ganal, M. and Nagy, I. (2009). Patterns of molecular evolution of microsatellite loci in pepper (Capsicum spp.) revealed by allele sequencing. Plant Syst. Evol. 281: 251–254
Tam, S. M., Lefebvre, V., Palloix, A., Sage-Palloix, A. M., Mhiri, C. and Grandbastien, M. A. (2009). LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor. Appl. Genet. 119: 973–989.
Tanksley, S. D. and McCouch, S. R. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 277: 1063–1066.
Thul, S. T., Darokar, M. P., Shasany, A. K. and Khanuja, S. P. (2012). Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Mol Biotechnol. 51(2): 137–147.
Tilahun. S., Paramaguru, P. and Kannan Bapu, J. R. (2013). Genetic Diversity in Certain Genotypes of Chilli and Paprika as Revealed by RAPD and SSR Analysis. Asian J. Agric. Sci. 5(2): 25–31.
Votava, E. J., Nabhan, G. P. and Bosland, P. W. (2002). Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepin (Capsicum annuum var. glabriusculum). Conserv. Genet. 3: 123–129.
Wright, S. I., Bi, I. V., Schroeder, S. G., Yamasaki, M., Doebley, J. F., McMullen, M. D. and Gaut, B. S. (2005). The effects of arti?cial selection on the maize genome. Science. 308: 1310–1314.
Zohary, D. and Hopf, M. (2000). Domestication of plants in the old world. 3rd Edn. New York. Oxford University Press. 316pp.
Ado, S. G. (1990). Pepper Production Guide: Extension Publication Submitted to the Horticultural Crops Research Programme. I. A. R. Samaru, p. 12.
Aguilar-Meléndez, A., Morrell, P. L., Roose, M. L. and Kim S.-C. (2009). Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am. J. Bot. 96(6): 1190–1202.
Bosland, P. W. and Votava, E. (1999). Peppers: Vegetable and Spices Capsicums. Oxford, UK: CABI Publishing. 204pp.
Baral, J. and Bosland, P. W. (2002). Genetic diversity of a Capsicum germplasm collection from Nepal as determined by Randomly Amplified Polymorphic DNA markers. J. Amer. Soc. Hort. Sci. 127(3): 316–324.
Buckler, E. S., Thornsberry, J. M. and Kresovich, S. (2001). Molecular diversity, structure and domestication of grasses. Genet. Res. 77: 213–218.
Dellaporta, S. L., Wood, J. and Hicks, J. B. (1983). “A plant DNA mini-preparation: version II. Plant Mol. Biol. Rep. 1(4): 19–21.
DeWitt, D. and Bosland, P. W. (1993). The pepper garden. Berkeley, California, Ten Speed Press. 209pp.
Djian-Caporalino, C., Lefebvre, V., Sage-Daubčze, A. M. and Palloix, A. (2007). Capsicum. In: Singh, R. J. and Jauhar, P. P. (eds.) Genetic resources, chromosome engineering and crop improvement. Vol. 3. Vegetable crops. CRC Press/Taylor and Francis Group, Boca Raton, p. 186–245.
Doebley, J. F., Gau, B. S. and Smith, B. D. (2006). The molecular genetics of crop domestication. Cell. 127: 1309–1321.
Erinle, I. D. (1989). Present status and prospects for?
increased production of tomato and pepper in Nigeria. In AVEDC Ed. Proc. Inter. I Sympt. Integrated Management Practices. p. 536–547.
González-Pérez, S., Garcés-Claver, A., Mallor, C., Sáenz de Miera, L. E., Fayos, O. Pomar, F. Merino, F and Silvar. C. (2014). New Insights into Capsicum spp Relatedness and the Diversification Process of C. annuum in Spain. 9(12): e116276.
Guzmán, F. A., Ayala, H., Azurdia, C., Duque, M. C., de Vicente, M. C. (2005). AFLP assessment of genetic diversity of Capsicum genetic resources in Guatemala: Home gardens as an option for conservation. Crop Sci. 45: 363–370.
Hernández-Verdugo, S., Luna-Reyes, R. and Oyama, K. (2001). Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Syst. Evol. 226(3): 129–142.
Hill, T. A., Ashra?, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M. J., Kozik, A., Michelmore, R. W., Van Deynze, A. (2013). Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip. PLoS One 8(2): e56200.
Lanteri, S., Acquadro, A. Quagliotti, L. and Portis. E. (2003). RAPD and AFLP assessment of genetic variation in a landrace of pepper (Capsicum annuum L.), grown in North-West Italy. Genet. Resour. Crop Ev. 50(7): 723–735.
Lee, J. M., Nahm, S. H., Kim, Y. M., Kim, B. D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor. Appl. Genet. 108: 619–627.
Odeigah, P. G. C., Oboh, B. and Aghalokpe, I. O. (1999). The characterization of Nigerian varieties of pepper, Capsicum annuum and Capsicum frutescens by SDS-polyacryl amide gel electrophoresis of seed proteins. Genet. Resour. Crop Ev. 46(2): 127–131.
Paran, I., Aftergoot, E. and Shifriss. C. (1998). Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica. 99(3): 167–173.
Pacheco-Olvera, A., Hernández-Verdugo, S., Rocha-Ramírez, V., González-Rodríguez, A. and Oyama, K. (2012). Genetic diversity and structure of pepper (Capsicum annuum L.) from NW Mexico analyzed by micro-satellite markers. Crop Sci. 52: 231–241.
Pickersgill B. (1997). Genetic resources and breeding of Capsicum spp. Euphytica. 96: 129–133.
Prince, J. P., Loaiza-Figueroa, F. and Tanksley, S. D. (1992). Restriction fragment length poly-morphism and genetic distance among Mexican accessions of Capsicum. Genome. 35: 726–732.
Rodriguez, J. M., Berke, T., Engle, L. and Nienhuis, J. (1999). Variation among and within Capsicum species revealed by RAPD markers. Theor. Appl. Genet. 99: 147–156.
Sneath, P. H. A. and Sokal, R. R. (1973). Numerical taxonomy. Freeman, San Francisco, CA, USA. 573pp.
Stágel, A., Gyurjan, I., Sasvari, Z., Lanteri, S., Ganal, M. and Nagy, I. (2009). Patterns of molecular evolution of microsatellite loci in pepper (Capsicum spp.) revealed by allele sequencing. Plant Syst. Evol. 281: 251–254
Tam, S. M., Lefebvre, V., Palloix, A., Sage-Palloix, A. M., Mhiri, C. and Grandbastien, M. A. (2009). LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor. Appl. Genet. 119: 973–989.
Tanksley, S. D. and McCouch, S. R. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 277: 1063–1066.
Thul, S. T., Darokar, M. P., Shasany, A. K. and Khanuja, S. P. (2012). Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers. Mol Biotechnol. 51(2): 137–147.
Tilahun. S., Paramaguru, P. and Kannan Bapu, J. R. (2013). Genetic Diversity in Certain Genotypes of Chilli and Paprika as Revealed by RAPD and SSR Analysis. Asian J. Agric. Sci. 5(2): 25–31.
Votava, E. J., Nabhan, G. P. and Bosland, P. W. (2002). Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepin (Capsicum annuum var. glabriusculum). Conserv. Genet. 3: 123–129.
Wright, S. I., Bi, I. V., Schroeder, S. G., Yamasaki, M., Doebley, J. F., McMullen, M. D. and Gaut, B. S. (2005). The effects of arti?cial selection on the maize genome. Science. 308: 1310–1314.
Zohary, D. and Hopf, M. (2000). Domestication of plants in the old world. 3rd Edn. New York. Oxford University Press. 316pp.
Published
2018-07-25
How to Cite
Adeyemo, O. A., & Lawal, O. (2018). Assessment of Genetic Diversity based on RAPD Analysis in Cultivars of Peppers (Capsicum annuum, Capsicum chinense and Capsicum frutescens) Grown in Nigeria. Journal of Scientific Research and Development, 17(1), 48-53. Retrieved from http://jsrd.unilag.edu.ng/article/view/38
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