Assessment of Genetic Diversity in Contrasting Sugarcane Varieties Using Inter-Simple Sequence Repeat (ISSR) Markers


Sugarcane is an important tropical crop, responsible for two thirds of the world sugar production, gaining actually importance as a source of biofuel. Drought tolerance is a very important feature considering the actual climate change scenario throughout the world. This study aimed to determine the genetic diversity between sugarcane varieties with contrasting features under drought. For this purpose, twelve ISSR primers were used to characterize nine sugarcane varieties under cultivation in different countries including selected drought resistant material from Northeast Brazil and two varieties from India as contrasting genotypes. 317 scorable bands were generated, among which 301 comprised polymorphic markers, with an average of 25 polymorphic bands per primer. In the generated dendrogram the accessions were placed in clusters, where cluster A included two varieties from India (Co331 and Co419), and B comprised plants eight Brazilian accessions and a ‘Barbado’ variety. Within this clade, drought tolerant and susceptible varieties were clearly separated. The present evaluation revealed important contrasting parental candidates regarding their drought response, very promising for future mapping approaches aiming the identification of quantitative trait loci (QTLs) associated to drought in sugarcane. The selected primers were used for the first time in sugarcane, representing valuable tools for future evaluations, with emphasis to diversity characterization and genetic mapping.

Share and Cite:

Costa, M. , Amorim, L. , Onofre, A. , Melo, L. , Oliveira, M. , Carvalho, R. and Benko-Iseppon, A. (2011) Assessment of Genetic Diversity in Contrasting Sugarcane Varieties Using Inter-Simple Sequence Repeat (ISSR) Markers. American Journal of Plant Sciences, 2, 425-432. doi: 10.4236/ajps.2011.23048.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] S. Srivastava and O. S. Gupta, “Inter Simple Sequence Repeat Profile as a Genetic Marker System in Sugarcane,” Sugar Tech, Vol. 10, No. 1, 2008, pp. 48-52. doi:10.1007/s12355-008-0008-y
[2] D. W. Cornland, F. X. Johnson, F. Yamba, E. N. Chidumayo, M. M. Morales, O. Kalumiana and S. B. Mtonga-Chidumayo, “Sugarcane Resources for Sustainable Development: A Case Study in Luena, Zambia,” Stockholm Environment Institute, Stockholm, 2001.
[3] K. S. Aitken, J. C. Li, P. Jackson, G. Piperidis and C. L. MCintyre, “AFLP Analysis of Genetic Diversity within Saccharum officinarum and Comparison with Sugarcane Cultivars,” Australian Journal of Agricultural Research, Vol. 57, No. 11, 2006, pp. 1167-1184. doi:10.1071/AR05391
[4] F. C. Atkin, M. J. Dieters and J. K. Stringer, “Impact of Depth of Pedigree and Inclusion of Historical Data on the Estimation of Additive Variance and Breeding Values in a Sugarcane Breeding Program,” Theoretical and Applied Genetics, Vol. 119, No. 3, 2009, pp. 555-565. doi:10.1007/s00122-009-1065-7
[5] A. D’Hont, P. S. Rao, P. Feldmann, L. Grivet, F. N. Islam, P. Taylor and J. C. Glaszmann, “Identification and Characterisation of Sugarcane Intergeneric Hybrids, Saccharum officinarum × Erianthus arundinaceus, with Molecular Markers and DNA in Situ Hybridisation,” Theoretical and Applied Genetics, Vol. 91, No. 2, 1995, pp. 320-326. doi:10.1007/BF00220894
[6] P. C. Bundock, F. G. Eliott, G. Ablett, A. D. Benson, R. E. Casu, K. S. Aitken and R. J. Henry, “Targeted Single Nucleotide Polymorphism (SNP) Discovery in a Highly Polyploid Plant Species Using 454 Sequencing,” Plant Biotechnology Journal, Vol. 7, No. 4, 2009, pp. 347-354. doi:10.1111/j.1467-7652.2009.00401.x
[7] S. K. Parida, K. K. Sanjay, K. Sunita, V. Dalal, G. Hemaprabha, A. Selvi, A. Pandit, A. Singh, K. Gaikwad, T. R. Sharma, P. S. Srivastava, N. K. Singh and T. Mohapatra, “Informative Genomic Microsatellite Markers for Efficient Genotyping Applications in Sugarcane,” Theoretical and Applied Genetics, Vol. 118, No. 2, 2009, pp. 327-338. doi:10.1007/s00122-008-0902-4
[8] S. L. Dillon, F. M. Shapter, R. J. Henry, G. Cordeiro, L. Izquierdo and S. L. Lee, “Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae),” Annals of Botany, Vol. 100, No. 5, 2007, pp. 975-989. doi:10.1093/aob/mcm192
[9] L. M. Raboin, J. Pauquet, M. Butterfield, A. D’Hont and J. C. Glaszmann, “Analysis of Genome-Wide Linkage Disequilibrium in the Highly Polyploid Sugarcane,” Theoretical and Applied Genetics, Vol. 116, No. 5, 2008, pp. 701-714. doi:10.1007/s00122-007-0703-1
[10] K. M. Oliveira, L. R. Pinto, T. G. Marconi, M. Mollinari, E. C. Ulian, S. M. Chabregas, M. C. Falco, W. Burnquist, A. A. F. Garcia and A. P. Souza, “Characterization of New Polymorphic Functional Markers for Sugarcane,” Genome, Vol. 52, No. 2, 2009, pp. 191-209. doi:10.1139/G08-105
[11] S. Creste, K. A. G. Accoroni, L. R. Pinto, R. Vencovsky, M. A. Gimenes, M. A. Xavier, M. G. A. Landell, “Genetic Variability among Sugarcane Genotypes Based on Polymorphisms in Sucrose Metabolism and Drought Tolerance Genes,” Euphytica, Vol. 172, No. 3, 2010, pp. 435-446. doi:10.1007/s10681-009-0078-2
[12] N. Jannoo, L. Grivet, M. Seguin, F. Paulet, R. Domaingue, P. S. Rao, A. Dookun, A. D’Hont and J. C. Glaszmann, “Molecular Investigation of the Genetic Base of Sugarcane Cultivars,” Theoretical and Applied Genetics, Vol. 99, No. 1, 1999, pp. 171-184. doi:10.1007/s001220051222
[13] P. G. Kawar, R. M. Devarumath and Y. Nerkar, “Use of RAPD Markers for Assessment of Genetic Diversity in Sugarcane Cutivars,” Indian Journal of Biotechnology, Vol. 8, No. 1, 2009, pp. 67-71.
[14] F. A. Khan, A. Khan, F. M. Azhar and S. Rauf, “Genetic Diversity of Saccharum officinarum Accessions in Pakistan as Revealed by Random Amplified Polymorphic DNA,” Genetics and Molecular Research, Vol. 8, No. 4, 2009, pp. 1376-1382. doi:10.4238/vol8-4gmr665
[15] M. L. Lima, A. A. Garcia, K. M. Oliveira, S. Matsuoka, H. Arizono, C. L. De Souza Jr. and A. P. De Souza, “Analysis of Genetic Similarity Detected by AFLP and Coefficient of Parentage among Genotypes of Sugar Cane (Saccharum spp.),” Theoretical and Applied Genetics, Vol. 104, No. 1, 2002, pp. 30-38. doi:10.1007/s001220200003
[16] S. Alwala, C. A. Kimbeng, K. A. Gravois and K. P. Bischoff, “Trap a New Tool for Sugarcane Breeding: Comparison with AFLP and Coefficient of Parentage,” Journal American Society of Sugar Cane Technologists, Vol. 26, No. 1, 2006, pp. 62-87.
[17] N. C Glynn, K. Mccorkl and J. C. Comstock, “Diversity among Mainland USA Sugarcane Cultivars Examined by SSR Genotyping,” Journal American Society of Sugar Cane Technologists, Vol. 29, No. 1, 2009, pp. 36-52.
[18] K. Weising, H. Nybom, K. Wolff and W. Meyer, “DNA Fingerprinting in Plants and Fungi,” CRC Press Inc., Boca Raton, 1995.
[19] A. M. Benko-Iseppon, P. Winter, B. Hüttel, F. J. Muehlbauer, C. Stagginus and G. Kahl, “Pathogen-Related Sequences around Fusarium Race 4 Resistance Locus in Chickpea Detected by DNA Amplification Fingerprinting (DAF),” Theoretical and Applied Genetics, Vol. 107, No. 2, 2003, pp. 379-386. doi:10.1007/s00122-003-1260-x
[20] S. D. Michaels, M. C. John and R. M. Amasino, “Removal of Polysaccharides from Plant DNA by Ethanol Precipitation,” Biotechniques, Vol. 17, No. 2, 1994, pp. 274-276.
[21] D. R. Ayres and D. R. Strong, “Origin and Genetic Diversity of Spartina anglica (Poaceae) Using Nuclear DNA Markers,” American Journal of Botany, Vol. 88, No. 10, 2001, pp. 1863-1867. doi:10.2307/3558362
[22] M. E. Fernández, A. M. Figueiras and C. Benito, “The Use of ISSR and RAPD Markers for Detecting DNA Polymorphism, Genotype Identification and Genetic Diversity among Barley Cultivars with Known Origin,” Theoretical and Applied Genetics, Vol. 104, No. 5, 2002, pp. 845-851. doi:10.1007/s00122-001-0848-2
[23] J. U. Jeung, H. G. Hwang, H. P. Moon and K. K. Jena, “Fingerprinting Temperate Japonica and Tropical Indica Genotypes by Comparative Analysis of DNA Markers,” Euphytica, Vol. 146, No. 3, 2005, pp. 239-251. doi:10.1007/s10681-005-9022-2
[24] F. J. Rohlf, “NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1,” Exeter Software, 2000.
[25] S. Kumar, K. Tamura and M. Nei, “MEGA 3: Integrated Software for Molecular Evolutionary Genetics Analysis and sequence Alignment, Version 3.1,” Briefings in Bioinformatics, Vol. 5, No. 2, 2004, pp. 150-163. doi:10.1093/bib/5.2.150
[26] D. M. Burner, Y. B. Pan and R. D. Webster, “Genetic Diversity of North American and Old World Saccharum Assessed by RAPD Analysis,” Genetic Resources and Crop Evolution, Vol. 44, No. 3, 1997, pp. 235-240. doi:10.1023/A:1008631731506
[27] N. V. Nair, A. Selvi, T. V. Sreenivasan and K. N. Pushpalatha, “Molecular Diversity in Indian Sugarcane Cultivars as Revealed by Randomly Amplified DNA Polymorphisms,” Euphytica, Vol. 127, No. 2, 2002, pp. 219-225. doi:10.1023/A:1020234428681
[28] C. M. Da Silva, C. A. Mangolin, A. S. Mott and M. F. P. S. Machado, “Genetic Diversity Associated with in Vitro and Conventional Bud Propagation of Saccharum Varieties Using RAPD Analysis,” Plant Breeding, Vol. 127, No. 2, 2008, pp. 160-165. doi:10.1111/j.1439-0523.2007.01438.x
[29] C. Schl?tterer and D. Tautz, “Slippage Synthesis of Simple Sequence DNA,” Nucleic Acids Research, Vol. 20, No. 2, 1992, pp. 211-215. doi:10.1093/nar/20.2.211
[30] L. Goul?o and C. M. Oliveira, “Molecular Characterization of Cultivars of Apple (Malus × domestica Borkh.) Using Microsatellite (SSR and ISSR) Markers,” Euphytica, Vol. 122, No. 1, 2001, pp. 81-89. doi:10.1023/A:1012691814643
[31] W. Qian, S. Ge and D. Y. Hong, “Genetic Variation within and among Populations of Wild Rice Oryza granulate from China Detected by RAPD and ISSR Markers,” Theoretical and Applied Genetics, Vol. 102, No. 2-3, 2001, pp. 440-449. doi:10.1007/s001220051665
[32] Y. C. Hou, Z. H. Yan, Y. M. Wei and Y. L. Zheng, “Genetic Diversity in Barley from West China Based on RAPD and ISSR Analysis,” Barley Genetics Newsletter, Vol. 35, No. 1, 2005, pp. 9-22.
[33] R. R. Gomes-Filho and J. F. Tahin, “Respostas Fisiológicas de Cultivares de Caupi (Vigna unguiculata L.) Eretos e Decumbentes a Diferentes Níveis de Irriga??o,” Engenharia Agrícola, Vol. 10, No. 1, 2002, pp. 56-60.
[34] C. Pimentel, B. Sarr, O. Diouf, A. C. Z. Abboud and H. Roy-Macauley, “Tolerancia Protoplasmática Foliar à Seca, em Dois Genótipos de Caupi Cultivados em Campo,” Revista Universidade Rural, Vol. 22, No. 1, 2002, pp. 7-14.
[35] L. Zeng, T. R. Kwon, X. Liu, C. Wilson, C. M. Grieve and G. B. Gregorio, “Genetic Diversity Analyzed by Microsatellite Markers among Rice Genotypes with Different Adaptations to Saline Soils,” Plant Science, Vol. 166, No. 5, 2004, pp. 1275-1285. doi:10.1016/j.plantsci.2004.01.005
[36] S. Virupakshi and G. R. Naik, “ISSR Analysis of Chloroplast and Mitochondrial Genome Can Indicate the Diversity in Sugarcane Genotypes for Red Rot Resistance,” Sugar Tech, Vol. 10, No. 1, 2008, pp. 65-70. doi:10.1007/s12355-008-0011-3
[37] A. Selvi, N. V. Nair, J. L. Noyer, N. K. Singh, K. C. Balasundaram, K. C. Bansal, K. R. Koundal and T. Mohapatra, “Genomic Constitution and Genetic Relationship among the Tropical and Subropical Indian Sugarcane Cultivars Revealed by AFLP,” Crop Science, Vol. 45, No. 5, 2005, pp. 1750-1757. doi:10.2135/cropsci2004.0528
[38] J. Bao, H. Corke and M. Sun, “Analysis of Genetic Diversity and Relationships in Waxy Rice (Oryza sativa L.) Using AFLP and ISSR Markers,” Genetic Resources and Crop Evolution, Vol. 53, No. 2, 2006, pp. 323-330. doi:10.1007/s10722-004-6145-6

Copyright © 2024 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.