Genetic diversity assessment in Indian cultivated pea (Pisum sativum L.) varieties using RAPD markers
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Abstract
In the present study, the genetic diversity and inter-relationships among 12 varieties of pea were analyzed by using RAPD markers. A total of 118 bands were generated with 20 RAPD primers, of which 107 bands were polymorphic (90.81%). The PIC value ranged from 0.602-0.863 with an average of 0.754. High level of polymorphism and low genetic similarity within pea varieties suggested that they have a high level of genetic diversity. Unique RAPD fragments (700bp-1500bp) were also observed in five varieties i.e., AP-01, Aparna, Uttra, Rachna and Rachna-1D. In the dendrogram, 12 varieties were broadly grouped into 2 main clusters consisting of 5 (Cluster-I) and 4 (Cluster-II) varieties, respectively, while other three varieties i.e., KPMR-522, Aparna and AP-03 were out of group. In cluster-I, Ambika and AP-01 and Rachna and Vikas showed 62% and 58% similarities whereas, HUDP-15 grouped with 56% similarities with rest two varieties. In cluster II, Uttara and Prakash showed maximum similarity (65%) whereas, Rachna1-D showed (58%) similarities with them. KPMR-400 showed 52% similarity in this group. KPMR-400, Aparna and AP-03 were more diverse in comparison to others. A two-dimensional plot generated from principal co-ordinate analysis of RAPD data also supported the clustering pattern of dendrogram. This study indicated the presence of high genetic diversity among pea varieties, which could be used for developing core collections of pea germplasm for breeding and germplasm management purposes.
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Keywords
Genetic diversity, Pea, PCA, RAPD, UPGMA
References
Ahmad, G., Mudasir., Kudesia, R., Shikha and Srivastava, M.K. (2010). Evaluation of genetic diversity in Pea (Pisum sativum L) using RAPD analysis. Genetic Engineering & Biotechnology Journal, 16: 1-5.
Akond, M.A., Watanabe, N. and Furuta, Y. (2007). Exploration of genetic diversity among Xinjiang Triticum and Triticum ponicum by AFLP markers. Journal of Applied Genetics, 48: 25-33.
Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D. and Sorrells, M.E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36: 181-186.
Baranger, A., Aubert, G., Arnau, G., Laine, A.L., Deniot, G., Potier, J., Weinachter, C., Lejeune-Hénaut, I., Lallemand, J. and Burstin, J. (2004). Genetic diversity within Pisum sativum using protein and PCR-based markers. Theoretical and Applied Genetics, 108 (7): 1309-1321.
Choudhury, P.R., Tanveer, H. and Dixit, G.P. (2007). Identification and detection of genetic relatedness among important varieties of pea (Pisum sativum L.) grown in India. Genetica, 130: 183-191.
Cipriani, G., Bella, R. and Testolin, R. (1996). Screening of RAPD primers for molecular taxonomy and cultivar fingerprinting in genus Actinidia. Euphytica, 90: 169-174.
Doyle, J.J. and Doyle, J.L. (1990). Isolation of plant DNA from fresh tissues. Focus, 12: 13- 15.
FAOSTAT (2011). Online statistics database of the Food and Agriculture Organization of the United Nations, Statistics on dry peas and green peas, retrieved 3 November 2011 from http://faostat.fao.org/site/291/default. aspx.
Hoey, B.K., Crowe, K.R., Jones, V.M. and Polans, M.O. (1996). A phylogenetic analysis of Pisum based on morphological characters, allozyme and RAPD markers. Theoretical and Applied Genetics, 92: 92-100.
Indian Horticulture Database (2011). Online All India Area, Production and Productivity statistics database of Pea, National Horticulture Board, Ministry of Agriculture, Government of India, retrieved on September 20, 2013 from http://www.nhb.gov.in
Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin of the Society of Vaud Science National, 44: 223-270.
Kumar, S., Tamura, K., Jakobsen, I.B. and Nei, M. (2001). MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics, 17: 1244-1245.
Kwon, S., Brown, A.F., Hu, J., McGee, R., Watt, C., Kisha, T., Timmerman-Vaughan, G., Grusak, M., McPhee, K. E. and Coyne, C.J. (2012). Genetic diversity, population structure and genome-wide marker-trait association analysis emphasizing seed nutrients of the USDA pea (Pisum sativum L.) core collection. Genes and Genomics, 34: 305-320.
Lema-Ruminska, J., Zalewska, M. and Sadoch, Z. (2004). Radiomutants of Chrysanthemum of the lady group: RAPD analysis of the genetic diversity. Plant Breed-ing, 123: 290-292.
Lima-Brito, J., Carvalho, A., Martin, A., Heslop-Harrison, J.S. and Guedes-Pinto, H. (2006). Morphological, yield, cytological and molecular characterization of a breed wheat × tritorderm F1 hybrid. Journal of Genetics, 85: 123-131.
Mahasi, M.J., Wachira, F.N., Pathak, R.S. and Riungu, T.C. (2009). Genetic polymorphism in exotic safflower (Carthamus tinctorious L.) using RAPD markers. Journal of Plant Breeding and Crop Science, 1 (1): 8-12.
Mattagajasingh, I., Mukherjee, A.K. and Das, P. (2006). Genomic relations among 31 species of Mammillaria Haworth (Cactaceae) using random amplified polymorphic DNA. Z Naturforsch C, 61: 583-591.
Mukherjee, A.K., Dey, A., Acharya, L.K., Pallai, S.K. and Panda, P.C. (2013). Studies on genetic diversity in elite varieties of Chrysanthemum using RAPD and ISSR markers. Indian Journal of Biotechnology, 12: 161-169.
Petterson, D.S., Sipsas, S. and Mackintosh, J.B. (1997). The chemical composition and nutritive value of Australian grain legumes (2nd edn.) Grain Research and Development Corporation, Canberra, Australia.
Prevost, A.S. and Wilkinson, M.J. (1999). A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98: 107-112.
Raghunathachari, P., Khanna, V.K., Singh, U.S. and Singh, N.K. (2000). RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Current Science, 79 (7): 994 998.
Samatadze, T.E., Zelenina, D.A., Shostak, N.G., Volkov, A. A., Popov, K.V., Rachinskaya O.V., Borisov, A.Y., Tihonovich, I.A., Zelenin, A.V. and Muravenko, O.V. (2008). Comparative genome analysis in pea (Pisum sativum L.) Varieties and Lines with chromosomal and molecular markers. Russian Journal of Genetics, 44: 1424-1430.
Samec, P. and Našinec, B. (1996). The use of RAPD technique for the identification and classification of Pisum sativum L. genotypes. Euphytica, 89: 229-234.
Samec, P. and Nasinec, V. (1995). Detection of DNA polymorphism among pea cultivars using RAPD technique. Biologia Plantarum, 37: 321-327.
Simioniuc, D., Uptmoor, R., Friedt, W. and Ordon, F. (2002). Genetic diversity and relationships among pea cultivars revealed by RAPDs and AFLPs. Plant Breeding, 121: 429-435.
Taran, B., Zhang, C., Warkentin, T., Tullu, A. and Vandenberg, A. (2005). Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters. Genome, 48: 257-272.
Vand dar Maesen, L.I.G. (1990). Pigeon pea: Origin, History evolution and taxonomy, In The Pigeon Pea, Edited by Nene NL, Hall SD & Sheila VK (CAB International University Press, Wallingford, Oxon, UK), 15-46.
Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990a). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18: 6531-6535.
Williams, J.G.K., Hanafey, M.K., Rafalski, J.A. and Tingey, S.V., (1990b). Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology, 1218: 704-740.
Yadav, K., Singh, B.D., Srivastava, C.P., Chand, R. and Yadav, A. (2010). Analysis of genetic divergence in pea (Pisum sativum L.) using quantitative traits and RAPD markers. Indian Journal of Genetics, 70 (4): 363-369.
Zong, X., Redden, R.J., Liu, Q., Wang, S., Guan, J., Liu, J., Xu, Y., Liu, X., Gu, J., Yan, L., Ades, P. and Ford, R. (2009). Analysis of a diverse global Pisum sp. collections and comparison to a Chinese local Pisum sativum L. collection with microsatellite markers. Theoretical and Applied Genetics, 118(2), 193-204.
Akond, M.A., Watanabe, N. and Furuta, Y. (2007). Exploration of genetic diversity among Xinjiang Triticum and Triticum ponicum by AFLP markers. Journal of Applied Genetics, 48: 25-33.
Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D. and Sorrells, M.E. (1993). Optimizing parental selection for genetic linkage maps. Genome, 36: 181-186.
Baranger, A., Aubert, G., Arnau, G., Laine, A.L., Deniot, G., Potier, J., Weinachter, C., Lejeune-Hénaut, I., Lallemand, J. and Burstin, J. (2004). Genetic diversity within Pisum sativum using protein and PCR-based markers. Theoretical and Applied Genetics, 108 (7): 1309-1321.
Choudhury, P.R., Tanveer, H. and Dixit, G.P. (2007). Identification and detection of genetic relatedness among important varieties of pea (Pisum sativum L.) grown in India. Genetica, 130: 183-191.
Cipriani, G., Bella, R. and Testolin, R. (1996). Screening of RAPD primers for molecular taxonomy and cultivar fingerprinting in genus Actinidia. Euphytica, 90: 169-174.
Doyle, J.J. and Doyle, J.L. (1990). Isolation of plant DNA from fresh tissues. Focus, 12: 13- 15.
FAOSTAT (2011). Online statistics database of the Food and Agriculture Organization of the United Nations, Statistics on dry peas and green peas, retrieved 3 November 2011 from http://faostat.fao.org/site/291/default. aspx.
Hoey, B.K., Crowe, K.R., Jones, V.M. and Polans, M.O. (1996). A phylogenetic analysis of Pisum based on morphological characters, allozyme and RAPD markers. Theoretical and Applied Genetics, 92: 92-100.
Indian Horticulture Database (2011). Online All India Area, Production and Productivity statistics database of Pea, National Horticulture Board, Ministry of Agriculture, Government of India, retrieved on September 20, 2013 from http://www.nhb.gov.in
Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin of the Society of Vaud Science National, 44: 223-270.
Kumar, S., Tamura, K., Jakobsen, I.B. and Nei, M. (2001). MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics, 17: 1244-1245.
Kwon, S., Brown, A.F., Hu, J., McGee, R., Watt, C., Kisha, T., Timmerman-Vaughan, G., Grusak, M., McPhee, K. E. and Coyne, C.J. (2012). Genetic diversity, population structure and genome-wide marker-trait association analysis emphasizing seed nutrients of the USDA pea (Pisum sativum L.) core collection. Genes and Genomics, 34: 305-320.
Lema-Ruminska, J., Zalewska, M. and Sadoch, Z. (2004). Radiomutants of Chrysanthemum of the lady group: RAPD analysis of the genetic diversity. Plant Breed-ing, 123: 290-292.
Lima-Brito, J., Carvalho, A., Martin, A., Heslop-Harrison, J.S. and Guedes-Pinto, H. (2006). Morphological, yield, cytological and molecular characterization of a breed wheat × tritorderm F1 hybrid. Journal of Genetics, 85: 123-131.
Mahasi, M.J., Wachira, F.N., Pathak, R.S. and Riungu, T.C. (2009). Genetic polymorphism in exotic safflower (Carthamus tinctorious L.) using RAPD markers. Journal of Plant Breeding and Crop Science, 1 (1): 8-12.
Mattagajasingh, I., Mukherjee, A.K. and Das, P. (2006). Genomic relations among 31 species of Mammillaria Haworth (Cactaceae) using random amplified polymorphic DNA. Z Naturforsch C, 61: 583-591.
Mukherjee, A.K., Dey, A., Acharya, L.K., Pallai, S.K. and Panda, P.C. (2013). Studies on genetic diversity in elite varieties of Chrysanthemum using RAPD and ISSR markers. Indian Journal of Biotechnology, 12: 161-169.
Petterson, D.S., Sipsas, S. and Mackintosh, J.B. (1997). The chemical composition and nutritive value of Australian grain legumes (2nd edn.) Grain Research and Development Corporation, Canberra, Australia.
Prevost, A.S. and Wilkinson, M.J. (1999). A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98: 107-112.
Raghunathachari, P., Khanna, V.K., Singh, U.S. and Singh, N.K. (2000). RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Current Science, 79 (7): 994 998.
Samatadze, T.E., Zelenina, D.A., Shostak, N.G., Volkov, A. A., Popov, K.V., Rachinskaya O.V., Borisov, A.Y., Tihonovich, I.A., Zelenin, A.V. and Muravenko, O.V. (2008). Comparative genome analysis in pea (Pisum sativum L.) Varieties and Lines with chromosomal and molecular markers. Russian Journal of Genetics, 44: 1424-1430.
Samec, P. and Našinec, B. (1996). The use of RAPD technique for the identification and classification of Pisum sativum L. genotypes. Euphytica, 89: 229-234.
Samec, P. and Nasinec, V. (1995). Detection of DNA polymorphism among pea cultivars using RAPD technique. Biologia Plantarum, 37: 321-327.
Simioniuc, D., Uptmoor, R., Friedt, W. and Ordon, F. (2002). Genetic diversity and relationships among pea cultivars revealed by RAPDs and AFLPs. Plant Breeding, 121: 429-435.
Taran, B., Zhang, C., Warkentin, T., Tullu, A. and Vandenberg, A. (2005). Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters. Genome, 48: 257-272.
Vand dar Maesen, L.I.G. (1990). Pigeon pea: Origin, History evolution and taxonomy, In The Pigeon Pea, Edited by Nene NL, Hall SD & Sheila VK (CAB International University Press, Wallingford, Oxon, UK), 15-46.
Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990a). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18: 6531-6535.
Williams, J.G.K., Hanafey, M.K., Rafalski, J.A. and Tingey, S.V., (1990b). Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology, 1218: 704-740.
Yadav, K., Singh, B.D., Srivastava, C.P., Chand, R. and Yadav, A. (2010). Analysis of genetic divergence in pea (Pisum sativum L.) using quantitative traits and RAPD markers. Indian Journal of Genetics, 70 (4): 363-369.
Zong, X., Redden, R.J., Liu, Q., Wang, S., Guan, J., Liu, J., Xu, Y., Liu, X., Gu, J., Yan, L., Ades, P. and Ford, R. (2009). Analysis of a diverse global Pisum sp. collections and comparison to a Chinese local Pisum sativum L. collection with microsatellite markers. Theoretical and Applied Genetics, 118(2), 193-204.
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Genetic diversity assessment in Indian cultivated pea (Pisum sativum L.) varieties using RAPD markers. (2015). Journal of Applied and Natural Science, 7(1), 316-323. https://doi.org/10.31018/jans.v7i1.608
