AJPS  Vol.7 No.15 , November 2016
Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China
Abstract: Genetic variability among sugarcane genotypes from the Karst region of China was evaluated using genotype-specific microsatellite (SSR) markers. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred locally were screened for genetic variability with 21 SSR primer pairs. All the primer pairs were highly polymorphic and amplified a total of 167 alleles with an average of eight alleles per primer pair. The average polymorphism information content (PIC) value was 0.86 with a range of 0.68 and 0.92. A UPGMA dendrogram categorized the 18 sugarcane genotypes into three major groups containing three, ten and five genotypes, respectively. No geographical affinity was observed among genotypes within the same group. Eight SSR primer pairs produced cultivar-specific alleles, of which five alleles were unique to the QT-series clones, namely, SMC334BS-165 and SMC851MS-145 in QT 08-558, mSSCIR43-229 in QT 4, SM597CS-182 in QT 08-536 and SMC7CUQ-168 in QT 06-212. The clone-specific SSR alleles will be useful in identifying elite QT-series clones for use in the sugarcane crossing programs in China.
Cite this paper: Fu, Y. , Pan, Y. , Lei, C. , P. Grisham, M. , Yang, C. and Meng, Q. (2016) Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China. American Journal of Plant Sciences, 7, 2209-2220. doi: 10.4236/ajps.2016.715195.

[1]   Pan, Y.-B., Burner, D.M. and Legendre, B.L. (2000) An Assessment of the Phylogenetic Relationship among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5S rRNA Intergenic Spacers. Genetica, 108, 285-295.

[2]   Jannoo, N., Grivet, L., Seguin, M., Paulet, F., Domaingue, R., Rao, P.S., Dookun, A., D’Hont, A. and Glaszmann, J.C. (1999) Molecular Investigation of the Genetic Base of Sugarcane Cultivars. Theoretical and Applied Genetics, 99, 171-184.

[3]   Grivet, L., D’Hont, A., Roques, D., Feldmann, P., Lanaud, C. and Glaszmann, J.C. (1996) RFLP Mapping in Cultivated Sugarcane (Saccharum spp.): Genome Organization in a Highly Polypoid and Aneuploid Interspecific Hybrid. Genetics, 142, 987-1000.

[4]   Nair, N.V., Selvi, A., Sreenivasan, T.V. and Pushpalatha, K.N. (2002) Molecular Diversity in Indian Sugarcane Cultivars as Revealed by Randomly Amplified DNA Polymorphisms. Euphytica, 127, 219-225.

[5]   Burner, D.M., Pan, Y.-B. and Webster, R.D. (1997) Genetic Diversity of New World and Old World Saccharum Assessed by RAPD Analysis. Genetic Resources and Crop Evolution, 44, 235-240.

[6]   Pan, Y.-B., Burner, D.M., Ehrlich, K.C., Grisham, M.P. and Wei, Q. (1997) Analysis of Primer-Derived, Non-Specific Amplification Products in RAPD-PCR. BioTechniques, 22, 1072-1074.

[7]   Pan, Y.-B., Burner, D.M., Legendre, B.L., Grisham, M.P. and White, W.H. (2004) An Assessment of the Genetic Diversity within a Collection of Saccharum spontaneum with RAPD-PCR. Genetic Resources and Crop Evolution, 51, 895-903.

[8]   Aitken, K.S., Jackson, P.A. and McIntyre, C.L. (2005) A Combination of AFLP and SSR Markers Provides Extensive Map Coverage and Identification of Homo(eo)logous Linkage Groups in a Sugarcane Cultivar. Theoretical and Applied Genetics, 110, 789-801.

[9]   Besse, P., Taylor, G., Carroll, B., Berding, N., Burner, D.M. and McIntyre, C.L. (1998) Assessing Genetic Diversity in a Sugarcane Germplasm Collection Using an Automated AFLP Analysis. Genetica, 104, 143-153.

[10]   Lima, M.L.A., Garcia, A.A.F., Oliveira, K.M., Matsuoka, S., Arizono, H., de Souza Jr., C.L. and de Souza, A.P. (2002) Analysis of Genetic Similarity Detected by AFLP and Coefficient of Parentage among Genotypes of Sugar Cane (Saccharum spp.). Theoretical and Applied Genetics, 104, 30-38.

[11]   Cordeiro, G.M., Taylor, G.O. and Henry. R.J. (2000) Characterization of Microsatellite Markers from Sugarcane (Saccharum spp.). A Highly Polyploidy Species. Plant Science, 155, 161-168.

[12]   Da Silva J.A.G. (2001) Preliminary Analysis of Microsatellite Markers Derived from Sugarcane Expressed Sequence Tags (ESTs). Genetics and Molecular Biology, 24, 155-159.

[13]   Pan, Y.-B. (2006) Highly Polymorphic Microsatellite DNA Markers for Sugarcane Germplasm Evaluation and Variety Identity Testing. Sugar Tech, 8, 246-256.

[14]   Pan, Y.-B., Cordeiro, G.M., Richard Jr., E.P. and Henry, R.J. (2003) Molecular Genotyping of Sugarcane Clones with Microsatellite DNA Markers. Maydica, 48, 319-329.

[15]   Alwala, S., Suman, A., Arro, J.A., Veremis, J.C. and Kimbeng, C.A. (2006) Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity in Sugarcane Germplasm Collections. Crop Science, 46, 448-455.

[16]   Arro, J.A. (2004) Genetic Diversity among Sugarcane Clones Using Target Region Amplification Polymorphism (TRAP) Markers and Pedigree Relationships. Master’s Thesis, Louisiana State University, Baton Rouge.

[17]   Suhail, K.M., Yadava, S., Srivastava, S., Swapna, M., Chandra, A. and Singh, R.K. (2011) Development and Utilization of Conserved-Intron Scanning Marker in Sugarcane. Australian Journal of Botany, 59, 38-45.

[18]   Chandra, A., Jain, R., Solomon, S., Shrivastava, S. and Roy, A.K. (2013) Exploiting EST Databases for the Development and Characterisation of 3425 Gene-Tagged CISP Markers in Biofuel Crop Sugarcane and Their Transferability in Cereals and Orphan Tropical Grasses. BMC Research Notes, 6, 47.

[19]   Cordeiro, G.M., Eliott, F., McIntyre, C.L., Manners, J.M. and Henry, R.J. (2006) Characterization of Single Nucleotide Polymorphisms in Sugarcane ESTs. Theoretical and Applied Genetics, 113, 331-343.

[20]   Devarumath, R., Kalwade, S., Bundock, P., Eliott, F.G. and Henry, R. (2013) Independent Target Region Amplification Polymorphism and Single-Nucleotide Polymorphism Marker Utility in Genetic Evaluation of Sugarcane Genotypes. Plant Breeding, 132, 736-747.

[21]   Chandra, A., Grisham, M.P. and Pan, Y.-B. (2014) Allelic Divergence and Cultivar-Specific SSR Alleles Revealed by Capillary Electrophoresis Using Fluorescence-Labeled SSR Markers in Sugarcane. Genome, 57, 363-372.

[22]   Pan, Y.-B., Burner, D.M. and Wei, Q. (2001) Developing Species-Specific DNA Markers to Assist in Sugarcane Breeding. Proceedings of International Society of Sugar Cane Technologists, 24, 337-342.

[23]   Selvi, A., Nair, N.V., Noyer, J.L., Singh, N.K., Balasundaram, N., Bansal, K.C., Koundal, K.R. and Mohapatra, T. (2006) AFLP Analysis of the Phenetic Organization and Genetic Diversity in the Sugarcane Complex, Saccharum and Erianthus. Genetic Resources and Crop Evolution, 53, 831-842.

[24]   Maccheroni, W., Jordao, H., De Gaspari, R., De Moura, G.L. and Matsuoka, S. (2009) Development of a Dependable Microsatellite-Based Fingerprinting System for Sugarcane. Proceedings of the International Society of Sugar Cane Technologistics, 27, 47-52.

[25]   Oliveira, K.M., Pinto, L.R., Marconi, T.G., Mollinari, M., Ulian, E.C., Chabregas, S.M., Falco, M.C., Burnquist, W., Garcia, A.A. and Souza, A.P. (2009) Characterization of New Polymorphic Functional Markers for Sugarcane. Genome, 52, 191-209.

[26]   Pinto, L.R., Oliveira, K.M., Ulian, E.C., Garcia, A.A. and Souza, A.P. (2004) Survey in the Expressed Sequence Tag Database (SUCEST) for Simple Sequence Repeats. Genome, 47, 795-804.

[27]   Pinto, L.R., Oliveira, K.M., Marconi, T.G., Garcia, A.F., Ulian, E.C. and Souza, A.P. (2006) Characterization of Novel Sugarcane Expressed Sequence Tag Microsatellites and Their Comparison with Genomic SSRs. Plant Breeding, 125, 378-384.

[28]   Oliveira, K.M., Pinto L.R., Marconi, T.G., Margarido, G.R.A., Pastina, M.M., L.H.M., Teixeira, Figueira, A.V., Ulian, E.C., Garcia, A.A.F. and Souza, A.P. (2007) Functional Integrated Genetic Linkage Map Based on EST-Markers for a Sugarcane (Saccharum spp.) Commercial Cross. Molecular Breeding, 20, 189-208.

[29]   Marconi, T.G., Costa, E.A., Miranda, H.R., Mancini, M.C., Cardoso-Silva, C.B., Oliveira, K.M., Pinto, L.R., Mollinari, M., Garcia, A.A.F. and Souza, A.P. (2011) Functional Markers for Gene Mapping and Genetic Diversity Studies in Sugarcane. BMC Research Notes, 4, 264.

[30]   Parida, S.K., Kalia, S.K., Kaul, S., Dalal, V., Hemprapha, G., Selvi, A., Pandit, A., Singh, A., Gaikwad, K., Sharma, T.R., Srivastava, P.S., Singh, N.K. and Mohapatra, T. (2008) Informative Genomic Microsatellite Markers for Efficient Genotyping Application in Sugarcane. Theoretical and Applied Genetics, 118, 327-338.

[31]   Tew, T.L. and Pan, Y.-B. (2010) Microsatellite (Simple Sequence Repeat) Marker-Based Paternity Analysis of a Seven-Parent Sugarcane Polycross. Crop Science, 50, 1401-1408.

[32]   Sharma, M.D., Dobhal, U., Singh, P., Kumar, S., Gaur, A.K., Singh, S.P., Jeena, A.S., Koshy, E.P. and Kumar, S. (2014) Assessment of Genetic Diversity among Sugarcane Cultivars Using Novel Microsatellite Markers. African Journal of Biotechnology, 13, 1444-1451.

[33]   Devarumath, R.M., Kalwade, S.B., Kawar, P.G. and Sushir, K.V. (2012) Assessment of Genetic Diversity in Sugarcane Germplasm Using ISSR and SSR Markers. Sugar Tech, 4, 334-344.

[34]   Santos, J.M.D., Filho, L.S.C.D., Soriano, M.L., Silva, P.P.D., Nascimento, V.X., Barbosa, G.V.D.S., Todaro, A.R., Neto, C.E.R.N. and Almeida, C. (2012) Genetic Diversity of the Main Progenitors of Sugarcane from the RIDESA Germplasm Bank Using SSR Markers. Industrial Crops and Products, 40, 145-150.

[35]   Liu, P., Chandra, A., Que, Y., Chen, P.-H., Grisham, M.P., White, W.H., Dalley, C.D., Tew, T.L. and Pan, Y.-B. (2016) Identification of QTLs Controlling Sucrose Content Based on an Enriched Genetic Linkage Map of Sugarcane (Saccharum spp. Hybrids) Cultivar “LCP 85-384”. Euphytica, 207, 527-549.

[36]   Liu, P., Que, Y. and Pan, Y.-B. (2011) Highly Polymorphic Microsatellite DNA Markers for Sugarcane Germplasm Evaluation and Variety Identity Testing. Sugar Tech, 13, 129-136.

[37]   Pan, Y.-B., Miller, J.D., Schnell, R.J., Richard Jr., E.P. and Wei, Q. (2003) Application of Microsatellite and RAPD Fingerprints in the Florida Sugarcane Variety Program. Sugar Cane International, 19-28.

[38]   Pan, Y.-B., Liu, P. and Que, Y. (2014) Independently Segregating Simple Sequence Repeats (SSR) Alleles in Polyploid Sugarcane. Sugar Tech, 17, 235-242.

[39]   Lu, X., Zhou, H., Pan, Y.-B., Chen, C.Y., Zhu, J.-R., Chen, P.-H., Cai, Q. and Chen, R.-K. Segregation Analysis of Microsatellite (SRR) Markers in Sugarcane Polyploids. Genetics and Molecular Research, 14, 18384-18395.

[40]   Milbourne, D., Meyer, R., Bradshaw, J.E., Baird, E., Bonar, N., Povan, J., Powell, W. and Waugh, R. (1997) Comparison of PCR Based Marker System the Analysis of Genetic Relationships in Cultivated Potato. Molecular Breeding, 3, 127-136.

[41]   Rohlf, F.J. (2000) NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System Version 2.1. Exeter Publishing Setauket, New York.

[42]   Pan, Y.-B., Scheffler, B.S. and Richard Jr., E.P. (2007) High-Throughput Genotyping of Commercial Sugarcane Clones with Microsatellite (SSR) DNA Markers. Sugar Tech, 9, 176-181.

[43]   Hameed, U., Pan, Y.-B., Muhammad, K., Afghan, S. and Iqbal, J. (2012) Use of Simple Sequence Repeat Markers for DNA Fingerprinting and Diversity Analysis of Sugarcane (Saccharum spp.) Cultivars Resistant and Susceptible to Red Rot. Genetics and Molecular Research, 11, 1195-1204.

[44]   Liang, J., Pan, Y.-B., Li, Y.-R., Fang, F.-X., Chao, W.-K. and You, J.-H. (2010) Genetic Diversity Assessment of Saccharum Species and Elite Cultivars from China Using SSR Markers. Guihaia, 30, 594-600.

[45]   Chen, P.H., Pan, Y.-B., Chen, R.-K., Xu, L.-P. and Chen, Y.-Q. (2009) SSR Marker-Based Analysis of Genetic Relatedness among Sugarcane Cultivars (Saccharum spp. Hybrids) from Breeding Programs in China and Other Countries. Sugar Tech, 11, 347-354.