Cover Image

Microsatellite Genetic Markers of Saccharrum spp., and Erianthus sp. on Their Hybrids

Mala Murianingrum(1), Taryono Taryono(2*), Rani Agustina Wulandari(3)

(1) Indonesian Sweetener and Fiber Crops Research Institute, Malang, East Java
(2) Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta
(3) Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta
(*) Corresponding Author


Progeny identification is the important step that should be done after hybridization. However, polyploidy, aneuploidy and the high chromosome segregation in sugarcane which results various phenotypic characteristics variation and environmental effects become limiting factors to identify the progenies based on morphological characteristic. Microsatellite as one of molecular marker which has codominance inheritance, multiallelic, abundant in the genome and does not influenced by environmental factor is the best tool to asses the crossing fidelity accurately. This research aimed to identify the possibility of genetic marker of Saccharum spp. and Erianthus sp. on their hybrid using microsatellite molecular marker. This study was carried out in Molecular Genetic laboratory, Indonesian Sweetener and Fiber Crops Research Institute (ISFCRI) Malang, from August 2016 to July 2017. Eighty-six (86) F1 intraspecific and interspecific progeny, three commercial sugarcane varieties (PSJT941, PS881 and VMC7616) and two wild types (S. spontaneum dan Erianthus sp.) were assessed genetically by three microsatellite markers. Identification of microsatellite genetic markers was conducted by comparing the visualization band results from electrophoresis of each male and female parent through their progenies. All primers could identify Saccharum spp. and Erianthus sp. genetic markers. There were one to eleven Saccharum spp. and Erianthus sp. genetic markers could be identified such as 2-11 PS881-specific alleles; 2-3 VMC7616-specific alleles; 1-5 PSJT941-specific alleles; two S. spontaneum-specific alleles and 1-2 Erianthus-specific alleles. These findings could be used as the advance genetic marker of microsatellite in sugarcane breeding to asses the cross fidelity.


Sugarcane; PSJT941; S. spontaneum; Erianthus sp.; Genetic marker; Microsatellite

Full Text:



Aitken, K., J. Li, L. Wang, C. Qing, Y.H. Fan and P. Jackson. 2007, Characterization of intergeneric hybrids of Erianthus rockii and Saccharum using molecular markers. Genetic Resources and Crop Evolution, 54, pp. 1395-1405.

Barbosa M.H.P., M.D.V. Resende, L.A.S. Dias and G.V.S. Barbosa. 2012. Genetic improvement of sugar cane for bioenergy: the Brazilian experience in network research with RIDESA. Crop Breed. Appl. Biotechnol, 12, pp. 87-98.

Bremer, G. 1961. Problem in breeding and cytology of sugarcane. Euphytica, 10, pp. 59-78.

Budhisantoso, H. 2012. The efficiency of parent selction and its cross combination on sugarcane breeding : a simulation approach. Dissertation. Gadjah Mada University. Yogyakarta. Indonesia.

Chandra, A., M.P. Grisham and Y.B. Pan. 2014. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane. Genome, 57, pp. 363-372.

Chen, S, W.K. Shen, G.H. Xu, X.M. Wu, Q.Q. Deng and Z.M. Dou. 2017. Assessment of genetic relationship and diversity among Chinese sugarcane parental clones using Scot and ISSR markers. Int. J. Agric. Biol., 19 (2), pp. 291-298.

Costa, P.M.A., C.F. Almeida, G. Silveira, B. Soarez, D.C.F. Baffa, L.A. Peternelli, L.L. Bhering and M.H.P. Barbosa. 2014. Selfing confirmation in sugarcane by using simple sequence repeat markers: an individual reciprocal recurrent selection scheme. Genetics and Molecular Research, 13 (4), pp. 8962-8970.

Daniels, J. and Roach, B.T.. 1987. Taxonomy and Evolution. In: D.J. Heinz, ed., Sugarcane Improvement Through Breeding, Published by Elsevier. Amsterdam. Vol 1., pp. 7–84.

D'Hont, A., L. Grivet, P. Fieldmann, S. Rao, N. Berding and J. C. Glaszmann. 1996, Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Molecular and General Genetics, 250, pp. 405-413.

Filho, L.S.C.D., P.P. Silva, J.M. Santos, G.V.S Barbosa, C.E. Ramalho-Neto, L. Soares, J.C.F. Andrade, C.Almeida. 2010. Genetic similarity among genotypes of sugarcane estimation by SSR and coefficient of parentage. Sugar Tech, 12(2), pp. 145-149.

Fu, D., A.S. Mason, M. Xiao and H. Yan. 2016. Effects of genome structure variation, homeologous genes and repetitive DNA on polyploidy crop research in the age of genomics. Plant Science, 242, pp. 37-46.

Gao, Y.J., X.H. Liu, R.H. Zhang, H. Zhou, J.X. Liao, W.X. Duan and G.M. Zhang. 2015. Verification of progeny from crosses between sugarcane (Saccharum spp.) and an intergeneric hybrid (Erianthus arundinaceus × Saccharum spontaneum) with molecular Markers. Sugar Tech, 17(1), pp. 31-35.

Govindaraj, P., A. Balamurugan and U.S. Natarajam. 2012. Indentification of intergeneric hybrid between Erianthus arundinaceus and Saccharum spontaneum through STMS markers. International Sugar Journal, 114(1361), pp. 350-356.

Grivet L and P. Arruda. 2001. Sugarcane genomics : depicting the complex genome of an important tropical crop. Current Opinion in Plant Biology, 5, pp. 122-127.

Hapsoro, D., H.A. Warganegara, S.D. Utomo, N. Sriyani and Yusnita. 2015. Genetic diversity among sugarcane (Saccharum officinarum L) genotypes as shown by randomly amplified polymorphic DNA (RAPD). Agrivita, 37(2), pp. 247-257.

Hogarth, D.M. 1987. Genetic of sugarcane. In: D.J. Heinz, ed., Sugarcane improvement through breeding. Amsterdam : Elsevier, pp. 255-268

Huang, Y., J. Wu, P. Wang, Y. Lin, C. Fu., Z. Deng, Q. Wang, Q. Li, R. Chen and M. Zhang. 2015. Characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp and Erinathus arundinaceus. Plos One, 10(7), pp. 1-13.

Janoo, N., L. Grivet, J. David, A. D’Hont and J.C. Glaszmann. 2004. Differential chromosome pairing affinities at meiosis in polyploidy sugarcane revealed by molecular markers. Heredity, 93, pp. 460-467.

Lu, X., H. Zhou, Y.B. Pan, C.Y. Chen, J.R. Zhu, P.H. Chen, Y.R. Li, Q. Cai and R.K. Chen. 2015. Segregation analysis of mikrosatelite (SSR) marker in sugarcane polyploid. Genetics and Molecular Research, 14(4), pp. 18384-18395.

Masom, A.S. and J.C. Pires. 2015. Unreduced gametes : meiotic mishap or evolutionary mechanism? Trends in Genetics, 31(1), pp. 5-10.

McIntyre, C.L. and P.A. Jackson. 2001. Low level of selfing found in a sample of crosses in Australian sugarcane breeding programs. Euphytica, 117, pp. 245–249.

Melloni, M.L.G., M.S. Scarpari, L.R. Pinto, D. Perecin, M.A. Xavier and M.G.A. Landell. 2014. Selfing rate estimation in sugarcane under unfavorable natural conditions of crossing by using microsatellite markers. Genetics and Molecular Research, 13(1), pp. 2278-2289.

Ming, R., S.C. Liu, Y.R. Lin, J. da Silva, W. Wilson, D. Braga, A. van Deynze, T. F. Wenslaff, K.K. Wu, P.H. Moore, W. Burnquist, M.E. Sorrells, J.E. Irvine and A.H. Peterson. 1998. Detaild alignment of Saccharum and Sorghum chromosomes : comparative organization of closely related diploid and polyploidy genomes. Genetic, 150, pp. 1663-1682.

Nagarajan, R., S. Alarmelu, R.M. Shanti and S. Dharmodharan. 2001. A note on extent selfing in interspesific crosses of Sacharum. Sugar Tech, 3(4), pp. 180-181.

Nair, N.V., A. Selvi, T.V. Sreenivasan, K.N. Pushpalathaand S Mary. 2006. Characterization of intergeneric hybrids of Saccharum using molecular markers. Genet Resour Crop Evol, 53, pp. 163–169.

Nair, N.V., K. Mahonraj, K. Sunadaravelpandian, A. Suganya, A. Selvi and C. Appunu. 2017. Characterization of an intergeneric hybrid of Erianthus procerus × Saccharum officinarum and its backcross progenies. Euphytica, 213(267), pp. 1-13

Organisation for Economic Co-operation and Development (OECD). 2013. Consensus Document on the Biology of Sugarcane (Saccharum spp). No.56. Environmet Directorate. Organisation for Economic Co-operation and Development. Paris

Pan, Y.B. 2006. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech, 8(4), pp. 246-256.

Pan, Y.B., G.M. Cordeiro, E.P. Richard Jr and R.J. Henry. 2003. Moleculer genotyping of sugarcane clones with microsatellite DNA markers. Maydica, 48, pp. 319-329.

Pan, Y.B., P. Liu dan Y.Que. 2015. Independent segregating simple sequence repeats (SSR) alleles in polyploidy sugarcane. Sugar Tech, 17(3), pp. 235-242.

Perera, M.F., M.E. Arias, D. Costilla, A.C. Luque, M.B. Garcı´a, C. Dı´az Romero, J. Racedo, S. Ostengo, M.P. Filippone, M.I. Cuenya and A.P. Castagnaro. 2012. Genetic diversity assessment and genotype identification in sugarcane based on DNA markers and morphological traits. Euphytica, 185, pp. 491–510.

Piperidis, G and A. D’Hont. 2001. Chromosome composition Analysis of Various Saccharum intrspecific hybrids by Genonic In Situ Hibridizaton (GISH). Proc.Int.Soc.Sugar Cane Technol., 24, pp. 565-566.

Piperedis, G., N. Piperedis and A. D’Hont. 2010. Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Mol Genet Genomic, 284, pp. 65-73.

Santos, J.M., G.V. de Souza Barbosa, C.E.R. Neto and C. Almeida. 2014. Efficiency of biparental crossing in sugarcane analyzed by SSR markers. Crop Breeding and Applied Biotechnology, 14, pp. 102-107.

Singh, R.K., R.B. Singh, S.P. Singh, and M.L. Sharma. 2011. Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica, 182, pp. 335–354.

Sreenivasan, T.V., B.S. Ahloowalia and D.J. Heinz. 1987. Cytogenetics. In: D.J. Heinz, ed., Sugarcane Improvement Through Breeding.(). Amsterdam: Elsevier, , pp. 211-253.

Stevenson, G.C. 1965. Genetics and Breeding of Sugarcane. London: Longmans, Green, , UK. pp.284

Tew, T.L. and Y.B. Pan. 2010. Microsatelite (simple sequence repeat) marker-based paternity analysis of a seven-parent sugarcane polycross. Crop Sci, 50, pp. 1401-1408.

Wang, X.H., Q.H. Yang, F.S. Li, L.L. He and S.C. He. 2009. Molecular indentification of Saccharum spp. × Erinathus fulvus hybrids using sequence-characterized amplified region markers. Crop Sci., 49, pp. 864–870.

Wu, J., Y. Huang, Y. Lin, C. Fu, S. Liu, Z. Deng, Q. Li, Z. Huang, R. Chen and M . Zhang. 2014. Unexpected inheritance pattern of Erianthus arundinaceus chromosomes in the intergeneric progeny between Saccharum spp and Erianthus arundinaceus. Plos One, 9(10), pp. 1-9.

Xavier, M.A., L.R. Pinto, T.M. Favero, D. Perecin, L.A. Carlini-Garcia and M.G.A. Landell. 2014. Paternity indentification in sugarcane polycross by using microsatelite markers. Genetics and Molecular Research, 13(1), pp. 2268-2277.

You, Q., L. Xu, Y. Zheng and Y. Que. 2013. Genetic diversity analysis of sugarcane parent in chinese breeding programmes using SSR markers. Hindawi Publishing Corporation. The Scientific World Journal, 2013, pp. 1-11.

Zhang, M.Q., A.L. Yu And R.K. Chen. 2001. Utility of SSRs for determining genetic similarities and relationships In Saccharum and its related Genera. Proc. Int. Soc. Sugar Cane Technol., 24, pp. 630-631.


Article Metrics

Abstract views : 2410 | views : 2287


  • There are currently no refbacks.