Assessment of the Utility of TRAP and EST-SSRs Markers for Genetic Diversity Analysis of Sugarcane Genotypes
- 18 Downloads
The TRAP and EST-SSRs technique were utilized for assessing the genetic diversity of 55 sugarcane genotypes (28 wildtypes and 27 cultivars). The total number of polymorphic bands amplified by TRAP primers ranged from 7 to 11 with an average of 9 amplified by SuSy + Arb2, SAI + Arb1, PPDK + Arb3 and PPDK+Arb2. The polymorphism was found to be high (≥50%), ranging from 78 to 100% with an average of 87% for all the markers. Polymorphic Information content (PIC) value ranged from 0.11 (SuSy+Arb2) to 0.44 (SuSy + Arb3) primers with an average of 0.27. Also, the highest resolving power (Rp) was found 6.9 in (SAI + Arb1) between nine primers. A total 15 sets of EST-SSRs primers were used for PCR amplification, 179 amplified fragments is produced which 174 were polymorphic. The total numbers of polymorphic alleles amplified by the various EST-SSRs markers were ranged from 5 (ESSR07 and ESSR10) to 22 (ESSR09), with an average of 13.5 alleles. The polymorphism was found to be high (≥50%), ranging from 83.33 to 100% with an average of 97.2% for all the markers Polymorphic Information content (PIC) value ranged from 0.29 (ESSR15) to 0.83 (ESSR04) primers with an average of 0.56. Also, the highest resolving power (Rp) was found in 8.55 ESSR05 between 15 primers. For the TRAP nine combination primers was used for the work. A total 85 amplified fragments were produced which 74 (85%) were polymorphic. In cooperation of both the markers, dendrogram was constructed using UPGMA method from the present study. Hence, the TRAP and EST-SSRs techniques jointly helped to identify the genetic diversity of sugarcane clones/varieties which could be used in breeding program for sugarcane improvement.
Keywords:sugarcane genetic diversity molecular assisted selection PIC TRAP EST-SSRs
The authors are grateful to the Director General, Vasantdada Sugar Institute (VSI), Pune for their constant support, encouragement and providing infrastructure facilities during research work and also thankful to Plant Breeding section, VSI for providing sugarcane leaf samples.
COMPLIANCE WITH ETHICAL STANDARDS
Conflict of interests. The authors declare that they have no conflict of interest.
Statement on the welfare of animals. This article does not contain any studies involving animals performed by any of the authors.
- 2.Roach, B.T., Nobilisation of sugarcane, Proc. Int. Soc. Sugar Cane Technot., 1972, vol. 14, pp. 206–216.Google Scholar
- 3.Daniels, J. and Roach, B.T., Taxonomy and evolution, in Sugarcane Improvement through Breeding, Heinz, D.J., Ed., Amsterdam: Elsevier Press, 1987, pp. 7–84.Google Scholar
- 7.Selvi, A., Nair, N.V., Noyer, J.L., Singh, N.K., Balasundaram, N., Bansal, K.C., Koundal, K.R., and Mohapatra, T., Genomic constitution and genetic relationship among the tropical and subtropical Indian sugarcane cultivars revealed by AFLP, Crop Sci., 2005, vol. 45, pp. 1750–1757.CrossRefGoogle Scholar
- 8.Kawar, P.G., Devarumath, R.M., and Nerkar, Y., Use of RAPD markers for assessment of genetic diversity in sugarcane cultivars. Indian J. Biotechnol., 2009, vol. 8, pp. 67–71.Google Scholar
- 9.Oliveira, K.M., Pinto, L.R., Marconi, T.G., Margarido, G.R.A., Pastina, M.M., Teixeira, L.H.M., Figueira, A.M., Ulian, E.C., Garcia, A.A.F., and Souza, A.P., Functional genetic linkage map on EST markers for a sugarcane (Saccharum spp.) commercial cross, Mol. Breed., 2007, vol. 20, pp. 189–208.CrossRefGoogle Scholar
- 10.Maccheroni, W., Jordao, H., De Gaspari, R., De Moura, G.L., and Matsuoka, S., Development of a dependable microsatellite-based fingerprinting system for sugarcane, Sugar Cane Int., 2009, vol. 27, pp. 47–52.Google Scholar
- 13.Kalwade, S.B., Devarumath, R.M., Kawar, P.G., and Sushir, K.V., Genetic profiling of sugar-cane genotypes using inter simple sequence repeat (ISSR) markers, Electron. J. Plant Breed., 2012, vol. 3, pp. 621–628.Google Scholar
- 15.Devarumath, R.M., Kalwade, S.B., Bundock, P., Elliott, F.G., and Henry, R., Independent target region amplification polymorphism and single-nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes, Plant Breed., 2013, vol. 132, pp. 736–747. doi.org/10.1111/pbr.12092Google Scholar
- 19.Singh, R.B., Singh, B., and Singh, R.K., Development of microsatellite (SSRs) markers and evaluation of genetic variability within sugarcane commercial varieties (Saccharum spp. hybrids), Int. J. Advanced Res., vol. 3, pp. 700–708.Google Scholar
- 23.Hu, J. and Vick, B., Target region amplification, polymorphism: a novel marker technique for plant genotypes, Plant Mol. Biol. Rep., vol. 20, pp. 289–294.Google Scholar
- 24.Suman, A., Ali, K., Arro, J., Parco, A.S., Kimbeng, C.A., and Baisakh, N., Molecular diversity among members of the Saccharum complex assessed using TRAP markers based on lignin-related genes, Bio. Energy Res., 2012, vol. 5, pp. 197–120.Google Scholar
- 26.Andru, S., Pan, Y.B., Thongthawee, S., Burner, D.M., and Kimbeng, C.A., Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers, Theor. Appl. Genet., 2011, vol. 123, pp. 77–93. doi 10.1007/s00122-011-1568-xCrossRefPubMedGoogle Scholar
- 28.Alwala, S., Kimbeng, C.A., Gravois, C.A., and Bischoff, K.P., TRAP, a new tool for sugarcane breeding: comparison with AFLP and coefficient of percentage. J. Am. Soc. Sugar Cane Technol., 2006b, vol. 26, pp. 62–87.Google Scholar
- 29.Da, SilvaJ.A. and Bressiani, J.A., Sucrose synthase molecular marker associated with sugar content in elite sugarcane progeny, Genet. Mol. Biol., 2005, vol. 28, pp. 294–298. doi.org/10.1590/S1415-47572005000200020Google Scholar
- 30.Aljanabi, S.M., Froget, L., and Dookun, A., An improved and rapid protocol for the isolation of polysaccharide and polyphenol free sugarcane DNA, Plant Mol. Biol. Rep., vol. 17, pp. 1–8.Google Scholar
- 32.Sambrook, J., Fritsch, E., and Maniatis, T., Molecular Cloning: A Laboratory Manual, New York, USA: Cold Spring Harbor, 1989.Google Scholar
- 33.Rohlf, F.J., NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, New York: Exeter Software, 2000.Google Scholar
- 34.Mateescu, R.G., Zhang, Z., Tgai, K., Phavaphutanon, J., Wursten, N.I., Lust, G., Quaa, R., Murphy, K., Acland, G.M., and Todhunter, R.J., Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for Hip dysplasia in crossbreed pedigree, J. Heredity, 2005, vol. 96, pp. 847–853.CrossRefGoogle Scholar
- 36.Filho, J.A.D., Resende, L.V., Bastos, G.Q., Neto, D.E.S., and Machado, P.R., Use of molecular markers RAPD, and ESTs SSR to study genetic variability in sugarcane, Rev. Cienc. Agron., 2013, vol. 44, pp. 141–149. doi.org/ 10.1590/S1806-66902013000100018Google Scholar
- 39.Hameed, U., Pan, Y.B., Muhammad, K., Afghan, S., and Iqbal, J., Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot, Genet. Mol. Res., 2012, vol. 11, pp. 1195–1204.CrossRefPubMedGoogle Scholar
- 40.Haq, S.U., Kumar, P., Singh, R.K., Kumar, S.V., Bhatt, B., Sharma, M., Kachhwaha, S., and Kothari, S.L., Assessment of functional EST-SSR markers (sugarcane) in cross-species transferability, genetic diversity among Poaceae plants, and bulk segregation analysis, Genet. Res. Int., 2016, pp. 1–16. doi.org/ 10.1155/2016/7052323Google Scholar
- 41.Marconi, T.G., Costa, E.A., Miranda, H., Mancini, M.C., Cardoso-Silva, C.B., Oliveira, K.M., Pinto, L.R., Mollinari, M., Garcia, A., and Sousa, A.P., Functional markers for gene mapping and genetic diversity studies in sugarcane, BMC Res. Notes, 2011, vol. 4, p. 264.CrossRefPubMedPubMedCentralGoogle Scholar
- 45.Khan, I.A., Bibi, S., Yasmeen, S., Seema, N., Khatri, A., Siddiqui, M.A., Nizamani, G.S., and Afgan, S., Identification of elite sugarcane clones through TRAP, Pak. J. Bot., 2011, vol. 43, pp. 261–269.Google Scholar
- 46.Glazmann, J.C., Lu, Y.H., and Lanaud, C., Variation of nuclear ribosomal DNA in sugarcane, J. Genet. Breed, 1990, vol. 44, pp. 191–198.Google Scholar
- 47.Singh, R.K., Singh, R., Singh, S.P., Mohapatra, T., and Singh, S.B., Molecular diversity among Saccharum species and elite sugarcane varieties based on RAPD and AFLP marers, Proc. Internl. Symp. on Technologies to improve Sugar Productivity in Developing Countries, Guillin, P. R. China, 2006, pp. 646–654.Google Scholar