Analysis of genetic diversity among tropical and subtropical maize inbred lines using SSR markers
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Abstract
Genetic diversity of 24 tropical and subtropical elite maize lines was assessed at molecular level employ-ing 42 Simple Sequence Repeats. A total of 107 alleles with an average of 2.55 alleles per locus were detected. The Polymorphism Information Content (PIC) values of 42 SSR loci ranged from 0.08 (UMC1428) to 0.68 (UMC2189 and UMC2332) with the overall calculated PIC mean value of 0.44, whereas the Discrimination Rate (DR) value for SSR markers ranged from 0.09 (UMC2089) to 0.42 (UMC1311) with the average DR value of 0.26. Pair-wise genet-ic similarity (GS) values, calculated by Jaccard’s coefficients, ranged between 0.25 and 0.78 with a mean genetic similarity of 0.63, indicating the existence of adequate amount of genetic divergence among the genotypes selected for the study. The cluster dendrogram separated all the inbred lines into six main clusters with sub clusters based on genetic similarity. Factorial analysis also confirmed a nearly similar pattern for grouping these inbred lines as pre-sented by cluster dendrogram. In this study, SSR markers were found to be powerful tool for detection of genetic diversity in maize inbred lines. These findings could provide information for effective utilization of these materials for development of maize hybrids as well as for genetic improvement of inbred lines.
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Keywords
Genetic diversity, Inbred lines, Maize, SSR markers, Polymorphism information content
References
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Almanza-Pinzon M.I., Khairallah, M., Fox P.N. and Warburton, M.L. (2003). Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions. Euphytica 130: 77-86.
Bantte, K. and Prasanna, B.M. (2003). Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines. Euphytica. 129: 337-344.
Barrett, B.A. and Kidwell, K.K. (1998). AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Science. 38: 1261-1271.
Beyene, Y., Botha, A. and Alexander, A.M. (2005). A comparative study of molecular and morphological methods of describing genetic relationships in traditional Ethiopian highland maize. African Journal of Biotechnology. 4(7): 586-595.
Parihar, C.M., Jat, S.L., Singh, A.K., Sai Kumar, R., Hooda, K.S., Chikkappa G.K. and Singh D.K. (2011). Maize Production Technologies in India. DMR Technical Bulletin2011/---. Directorate of Maize Research, Pusa Campus, New Delhi-110 012. Pp 30.
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Devi, P. and Singh N.K. (2011). Heterosis, molecular diversity, combining ability and their interrelationships in short duration maize (Zea mays L.) across the environments. Euphytica. 178: 71-81.
Enoki, H., Santo, H. and Koinuma, K. (2002). SSR analysis of genetic diversity among maize inbred lines adapted to cold region of Japan. Theoretical and Applied Genetics. 104: 1270-1277.
Goodman M.M, and Bird RMcK. (1977). The races of maize IV: tentative grouping of 219 Latin American races. Economic Botany. 31:204-221.
Gurung D.B., George M.L.C., and Dela Cruz Q.D. (2010). Analysis of Genetic Diversity within Nepalese Maize Populations Using SSR Markers. Nepal Journal of Science and Technology. 11: 1-8.
Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Societe Vaudoise Sciences Natureiies. 44: 223-270.
Jozsef P. and Zoltan L (2013). Global Socio-Economic and Environmental Dimensions of GM Maize Cultivation. Food and Nutrition Sciences. 4: 8-20.
Karanja, J., Amugune1, N.O., Ininda, J., Kimatu, J.N. and Damson, J.W. (2009). Microsatellite analysis of the correlation between molecular and morphological traits in assorted maize inbred lines. African Crop Science Journal. 12: 133-144.
Kassahun, B. and Prasanna, B.M. (2003). Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines. Euphytica. 129: 337-344.
Kostova, A., Todorovska E., Christov N., Hristov K., and Atanassov, A. (2006). Assessment of genetic variability induced by chemical mutagenesis in elite maize germplasm via SSR markers. Journal of Crop Improvement. 16: 37-48.
Legesse, B.W., Myburg, A.A., Pixely, K.V. and Botha, A.M. (2007). Genetic diversity of maize inbred lines revealed by SSR markers. Hereditas. 144: 10-17.
Lu Y., Yan J., Guimara˜es C.T., Taba S. and Hao Z. (2009). Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theoretical and Applied Genetics. 120: 93-115.
Moses A.A., Abebe M., Malaku G., Essie B., Vernon G., Eric D. and Ladejobi F. (2015). Diversity Assessment of Drought Tolerant Exotic and Adapted Maize (Zea mays L.) Inbred Lines with Microsatellite Markers. Journal of Crop Science and Biotechnology. 18 (3): 147-154.
Nepolean T., Singh I., Hossain F., Pandey N. and Gupta H.S. (2013). Molecular characterization and assessment of genetic diversity of inbred lines showing variability for drought tolerance in maize. Journal of Plant Biochemistry and Biotechnology. 22:71-79.
O’Donoughue, L.S., Souza, E., Tanksley, S.D. and Sorrells. M.E. (1994). Relationships among North American oat cultivars based on restriction fragment length polymorphisms. Crop Science. 34: 1251-1258.
Pedram K., Ghizan S., Jothi M.P., Nur A.P.A., and Ahmad S. (2012). Molecular characterization of tropical sweet corn inbred lines using microsatellite markers. Maydica. 57: 154-163.
Prasanna B.M. (2012). Diversity in global maize germplasm: characterization and utilization. Journal of Biosciences. 37: 843-55.
Prasanna, B.M. and Hoisington, D. (2003). Molecular breeding for maize improvement. An overview. Indian Journal of Biotechnology. 2: 85-98.
Pushpavalli, S.N.C.L., Sudan, C., Singh, N.N. and Prasanna, B.M. (2001). Differentiation of elite Indian maize hybrids using simple sequence repeat markers. Indian Journal of Genetics. 61: 304-308.
Revilla P., Soengas P., Malvar R.A., Cartea M.E. and Ordas A. (1998). Isozyme variation and historical relationships among the maize races of Spain. Maydica. 43:175-182.
Rohlf, F.J. (1989). In NTSYS-pc numerical taxonomy and multivariate analysis system. version 2.02, Exeter Publications, New York. USA.
Saghai-Maroof , M.A., Soliman, K.M., Jorgenson, R. and Allard, R.W. (1984). Ribosomal DNA spacer length polymorphism in barley. Mandelian inheritance, chromosomal location and population dynamics. Proceedings of the National Academy of Sciences of the United States of America. 81: 8014-8018.
Selvi, A., Nair, N.V., Noyer, J.L., Singh, N.K., Balasundarum, N., Bansal, K.C., Koundal, K.R. and Mohapatra, T. (2005). Genomic constitution and genetic relationship among the tropical and sub-tropical Indian sugarcane varieties revealed by AFLP. Crop Science. 45: 1750-1757.
Senior, M.L., Murphy, J.P., Goodman, M.M. and Stuber, C.W. (1998). Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Science. 38: 1088-1098.
Sharma, L., Prasanna, B.M. and Ramesh, B. (2010). Analysis of phenotypic and microsattelite-based diversity of maize landraces in India, especially from the North East Himalayan region. Genetica. 138: 619-631.
Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L., Mitchell S.E., Kresovich S. and Ziegle J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics. 95:163-173.
Soleimani, V.D., Baum B.R. and Johnson, D.A. (2002). AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. Theoretical and Applied Genetics. 104: 350-357.
Sun, G.L., William, M., Liu, J., Kasha, K.J. and Pauls, K.P. (2001). Microsatellite and RAPD polymorphisms in Ontario corn hybrids are related to the commercial sources and maturity ratings. Molecular Breeding,
7:13-24.
Tobias W., Eschholz Æ., Roland Peter Æ., Peter Stamp Æ., and Andreas H. (2008). Genetic diversity of Swiss maize (Zea mays L. ssp. mays) assessed with individuals and bulks on agarose gels. Genetic Resources and Crop Evolution. 55:971-983.
Vaz Patto, M.C., Satovic, Z., Pego, S. and Fevereiro, P. (2004). Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers. Euphytica. 137: 63-72.
Warburton, M.L., Xianchun, X., Crossa, J., Franco, J., Melchinger, A.E., Frisch, M., Bohn, M. and Hoisington, D. (2002). Genetic characterization of CIMMYT inbred maize lines and open pollinated populations using large scale fingerprinting methods. Crop Science. 42:1832-1840.
Yap, V.I. and Nelso, R.J. (1996). In WinBoot a programme for performing bootstrap analysis of binary data to determine the confidence limit of UPGMA-based dendogram, IRRI, Disc. Ser. No. 14. Int. Rice Rec. Inst., Manila, Philippines.
Ajmone Marsan P, Gorni C, Chitto` A, Redaelli R, Van Vijk R, Stam P, and Motto M. (2001). Identification of QTLs for grain yield and grain-related traits of maize (Zea mays L.) using an AFLP map, different testers, and cofactor analysis. Theor Appl Genet. 102: 230-243.
Almanza-Pinzon M.I., Khairallah, M., Fox P.N. and Warburton, M.L. (2003). Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions. Euphytica 130: 77-86.
Bantte, K. and Prasanna, B.M. (2003). Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines. Euphytica. 129: 337-344.
Barrett, B.A. and Kidwell, K.K. (1998). AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Science. 38: 1261-1271.
Beyene, Y., Botha, A. and Alexander, A.M. (2005). A comparative study of molecular and morphological methods of describing genetic relationships in traditional Ethiopian highland maize. African Journal of Biotechnology. 4(7): 586-595.
Parihar, C.M., Jat, S.L., Singh, A.K., Sai Kumar, R., Hooda, K.S., Chikkappa G.K. and Singh D.K. (2011). Maize Production Technologies in India. DMR Technical Bulletin2011/---. Directorate of Maize Research, Pusa Campus, New Delhi-110 012. Pp 30.
Dass, S., Jat, S.L., Chikkappa G.K., Parihar C.M., Kumar, B. and Singh A.K. (2012). Maize improvement towards food security: genetic and technological perspectives. In: conference programme book of 1st ICC India Grains Conference organized by ICC in partnership with ICRISAT at New Delhi from 16-18th January,
12: 24-25.
Devi, P. and Singh N.K. (2011). Heterosis, molecular diversity, combining ability and their interrelationships in short duration maize (Zea mays L.) across the environments. Euphytica. 178: 71-81.
Enoki, H., Santo, H. and Koinuma, K. (2002). SSR analysis of genetic diversity among maize inbred lines adapted to cold region of Japan. Theoretical and Applied Genetics. 104: 1270-1277.
Goodman M.M, and Bird RMcK. (1977). The races of maize IV: tentative grouping of 219 Latin American races. Economic Botany. 31:204-221.
Gurung D.B., George M.L.C., and Dela Cruz Q.D. (2010). Analysis of Genetic Diversity within Nepalese Maize Populations Using SSR Markers. Nepal Journal of Science and Technology. 11: 1-8.
Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Societe Vaudoise Sciences Natureiies. 44: 223-270.
Jozsef P. and Zoltan L (2013). Global Socio-Economic and Environmental Dimensions of GM Maize Cultivation. Food and Nutrition Sciences. 4: 8-20.
Karanja, J., Amugune1, N.O., Ininda, J., Kimatu, J.N. and Damson, J.W. (2009). Microsatellite analysis of the correlation between molecular and morphological traits in assorted maize inbred lines. African Crop Science Journal. 12: 133-144.
Kassahun, B. and Prasanna, B.M. (2003). Simple sequence repeat polymorphism in Quality Protein Maize (QPM) lines. Euphytica. 129: 337-344.
Kostova, A., Todorovska E., Christov N., Hristov K., and Atanassov, A. (2006). Assessment of genetic variability induced by chemical mutagenesis in elite maize germplasm via SSR markers. Journal of Crop Improvement. 16: 37-48.
Legesse, B.W., Myburg, A.A., Pixely, K.V. and Botha, A.M. (2007). Genetic diversity of maize inbred lines revealed by SSR markers. Hereditas. 144: 10-17.
Lu Y., Yan J., Guimara˜es C.T., Taba S. and Hao Z. (2009). Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theoretical and Applied Genetics. 120: 93-115.
Moses A.A., Abebe M., Malaku G., Essie B., Vernon G., Eric D. and Ladejobi F. (2015). Diversity Assessment of Drought Tolerant Exotic and Adapted Maize (Zea mays L.) Inbred Lines with Microsatellite Markers. Journal of Crop Science and Biotechnology. 18 (3): 147-154.
Nepolean T., Singh I., Hossain F., Pandey N. and Gupta H.S. (2013). Molecular characterization and assessment of genetic diversity of inbred lines showing variability for drought tolerance in maize. Journal of Plant Biochemistry and Biotechnology. 22:71-79.
O’Donoughue, L.S., Souza, E., Tanksley, S.D. and Sorrells. M.E. (1994). Relationships among North American oat cultivars based on restriction fragment length polymorphisms. Crop Science. 34: 1251-1258.
Pedram K., Ghizan S., Jothi M.P., Nur A.P.A., and Ahmad S. (2012). Molecular characterization of tropical sweet corn inbred lines using microsatellite markers. Maydica. 57: 154-163.
Prasanna B.M. (2012). Diversity in global maize germplasm: characterization and utilization. Journal of Biosciences. 37: 843-55.
Prasanna, B.M. and Hoisington, D. (2003). Molecular breeding for maize improvement. An overview. Indian Journal of Biotechnology. 2: 85-98.
Pushpavalli, S.N.C.L., Sudan, C., Singh, N.N. and Prasanna, B.M. (2001). Differentiation of elite Indian maize hybrids using simple sequence repeat markers. Indian Journal of Genetics. 61: 304-308.
Revilla P., Soengas P., Malvar R.A., Cartea M.E. and Ordas A. (1998). Isozyme variation and historical relationships among the maize races of Spain. Maydica. 43:175-182.
Rohlf, F.J. (1989). In NTSYS-pc numerical taxonomy and multivariate analysis system. version 2.02, Exeter Publications, New York. USA.
Saghai-Maroof , M.A., Soliman, K.M., Jorgenson, R. and Allard, R.W. (1984). Ribosomal DNA spacer length polymorphism in barley. Mandelian inheritance, chromosomal location and population dynamics. Proceedings of the National Academy of Sciences of the United States of America. 81: 8014-8018.
Selvi, A., Nair, N.V., Noyer, J.L., Singh, N.K., Balasundarum, N., Bansal, K.C., Koundal, K.R. and Mohapatra, T. (2005). Genomic constitution and genetic relationship among the tropical and sub-tropical Indian sugarcane varieties revealed by AFLP. Crop Science. 45: 1750-1757.
Senior, M.L., Murphy, J.P., Goodman, M.M. and Stuber, C.W. (1998). Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Science. 38: 1088-1098.
Sharma, L., Prasanna, B.M. and Ramesh, B. (2010). Analysis of phenotypic and microsattelite-based diversity of maize landraces in India, especially from the North East Himalayan region. Genetica. 138: 619-631.
Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L., Mitchell S.E., Kresovich S. and Ziegle J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics. 95:163-173.
Soleimani, V.D., Baum B.R. and Johnson, D.A. (2002). AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. Theoretical and Applied Genetics. 104: 350-357.
Sun, G.L., William, M., Liu, J., Kasha, K.J. and Pauls, K.P. (2001). Microsatellite and RAPD polymorphisms in Ontario corn hybrids are related to the commercial sources and maturity ratings. Molecular Breeding,
7:13-24.
Tobias W., Eschholz Æ., Roland Peter Æ., Peter Stamp Æ., and Andreas H. (2008). Genetic diversity of Swiss maize (Zea mays L. ssp. mays) assessed with individuals and bulks on agarose gels. Genetic Resources and Crop Evolution. 55:971-983.
Vaz Patto, M.C., Satovic, Z., Pego, S. and Fevereiro, P. (2004). Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers. Euphytica. 137: 63-72.
Warburton, M.L., Xianchun, X., Crossa, J., Franco, J., Melchinger, A.E., Frisch, M., Bohn, M. and Hoisington, D. (2002). Genetic characterization of CIMMYT inbred maize lines and open pollinated populations using large scale fingerprinting methods. Crop Science. 42:1832-1840.
Yap, V.I. and Nelso, R.J. (1996). In WinBoot a programme for performing bootstrap analysis of binary data to determine the confidence limit of UPGMA-based dendogram, IRRI, Disc. Ser. No. 14. Int. Rice Rec. Inst., Manila, Philippines.
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Analysis of genetic diversity among tropical and subtropical maize inbred lines using SSR markers. (2017). Journal of Applied and Natural Science, 9(4), 2427-2433. https://doi.org/10.31018/jans.v9i4.1549
