Skip to main content
SpringerLink
Log in

Analysis of Genetic Differentiation and Phylogenetic Relationships among Sugarcane Genotypes Differing in Response to Red Rot

  • Research Article
  • Published:
Sugar Tech Aims and scope Submit manuscript

Abstract

The selection of parents is the most crucial step in any breeding programme. A better understanding of genetic diversity among the available genotypes would help the breeder to make better crosses. Advancements of DNA marker techniques in many crops have supplemented the morphological traits with molecular markers to identify the diverse genotypes. The genetic diversity of 30 sugarcane genotypes differing in response to red rot resistance was carried out using simple sequence repeat (SSR) markers. The polymorphism information content (PIC) ranged from 0.216 to 0.813 with an average of 0.525. The highest values (0.86) of proportion of polymorphic loci (P) and expected heterozygosity (He) were obtained in the susceptible population (S) and moderately resistant population (MR), respectively. FST values between populations ranged from −0.043 to 0.041. However, AMOVA did not show much variation among the groups. Cluster analysis clearly distinguished all the genotypes from each other. The resistant genotypes namely ISH150 and SES594 emerged out to be most distinct genotypes, whereas the rest of the genotypes could be grouped in two broad clusters separating the moderately resistant and susceptible sugarcane genotypes. The clustering pattern was fairly supported by Mantel’s test (r = 0.894) and high bootstrap value (75.0%). Thus, information given in the present study can be used in genetic resource management as well as in broadening the genetic base of cultivated sugarcane for red rot and selection of suitable parent for generating the mapping population for tagging the red rot resistance gene(s) in sugarcane.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Aitken, K.S., P.A. Jackson, and C.L. McIntyre. 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.

    Article  CAS  PubMed  Google Scholar 

  • Ali, M.A., M.T. Seyal, S.I. Awan, S. Niaz, S. Ali, and A. Abbas. 2008. Hybrid authentication in upland cotton through RAPD analysis. Australian Journal of Crop Science 2(3): 141–149.

    CAS  Google Scholar 

  • Alwa, S., C.A. Kimbeng, K.A. Gravois, and K.P. Bischoff. 2006. TRAP, a new tool for sugarcane breeding: comparison with AFLP and coefficient of parentage. Journal American Society Sugar Cane Technologists 26: 62–85.

    Google Scholar 

  • Chen, F., D. Chen, Z. Gao, and X. Chen. 2010. Analysis of diversity in Chinese cultivated barley with simple sequence repeats: differences between eco-geographic populations. Biochemical Genetics 48: 44–56.

    Article  CAS  PubMed  Google Scholar 

  • Chona, B.L. 1954. Studies on the diseases of sugarcane in India. IV Relative resistance of sugarcane varieties to red rot. Indian Journal of Agricultural Sciences 24: 301–315.

    Google Scholar 

  • Cordeiro, G.M., R. Casu, C.L. McIntyre, J.M. Manners, and R.J. Henry. 2001. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and sorghum. Plant Science 160: 1115–1123.

    Article  CAS  PubMed  Google Scholar 

  • Cordeiro, G.M., Y.B. Pan, and R.J. Henry. 2003. Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Science 165: 181–189.

    Article  CAS  Google Scholar 

  • Daniels, J., and C.A. Daniels. 1976. A note on red rot disease. Physalospora tucumanensis Speg., and origin of sugarcane. Sugarcane Breeding News Letter 37: 17–19.

    Google Scholar 

  • Daniels, J., and B.T. Roach. 1987. Taxonomy and evolution. In Sugarcane Improvement through breeding, ed. D.J. Heinz, 7–84. Amsterdam: Elsevier Press.

    Chapter  Google Scholar 

  • D’Hont, A., D. Ison, K. Alix, C. Roux, and J.C. Glaszmann. 1998. Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41: 221–225.

    Article  Google Scholar 

  • Doyle, J.J., and J.L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13–14.

    Google Scholar 

  • Excoffier, L., P.E. Smouse, and J.M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: applications to human mitochondrial DNA restriction sites. Genetics 131: 479–491.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fregene, M., A. Bernal, M. Duque, A. Dixon, and J. Tohme. 2000. AFLP analysis of African cassava (Monihot esculenta Crantz). Theoretical and Applied Genetics 100: 673–685.

    Article  Google Scholar 

  • Govindaraj, P., U.S. Natarajan, N. Balasundaram, Premachandran, T.R. Sharma, K.R. Kaundal, K.C. Bansal, and N.K. Singh. 2005. Development of new microsatellite markers for identification of interspecific hybrids in sugarcane. Sugar Cane International 23: 30–34.

    CAS  Google Scholar 

  • Gupta, A.K., and V. Yadav. 2009. Evaluation of different sugarcane varieties for resistance against red rot disease. Environment and Ecology 27(3): 1006–1008.

    Google Scholar 

  • Hartl, D.L. 1987. A primer of population genetics, 2nd ed. Sunderland: Sinauer Associates Inc.

    Google Scholar 

  • Kirtkar, and H.S. Verma. 1963. Role of chemical in sugarcane disease control. Indian Sugar 13: 139–141.

    Google Scholar 

  • Lynch, M., and B.G. Milligan. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91–99.

    Article  CAS  PubMed  Google Scholar 

  • Mateescu, R.G., Z. Zhang, K. Tsai, J. Phavaphutanon, N.I. Burton-Wurster, G. Lust, R. Quaas, K. Murrphy, G.M. Acland, and R.J. Todhunter. 2005. Analysis of allele fidelity, polymorhic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree. Journal of Heredity 96: 847–853.

    Article  CAS  PubMed  Google Scholar 

  • Panje, R.R., and C.N. Babu. 1960. Studies in Saccharum spontaneum. Distribution and geographical associations of chromosome number. Cytologia 25: 152–172.

    Article  Google Scholar 

  • Pan, Y.B. 2006. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech 8: 246–256.

    Article  CAS  Google Scholar 

  • Pan, Y.B., J.D. Miller, R.J. Schnell Jr, E.P. Richard, and Q. Wei. 2003. Application of microsatellite and RAPD fingerprints in Florida sugarcane variety program. Sugarcane International 20: 19–24.

    Google Scholar 

  • Rohlf, F.J. 1998. NTSYS-PC numerical taxonomy and multivariate analysis system, version. Setauket, New York: Exeter Software.

    Google Scholar 

  • Schlotterer, C. 2004. The evolution of molecular markers-just matter of fashion? Nature Rev Genet 5: 63–69.

    Article  PubMed  Google Scholar 

  • Selvi, A., N. Mukunthan, R.M. Shanthi, P. Govindaraj, B. Singaravelu, and T.K. Prabu. 2008. Assessment of genetic relationships and marker identification in sugarcane cultivars with different levels of top borer resistance. Sugar Tech 10: 53–59.

    Article  CAS  Google Scholar 

  • Selvi, A., N.V. Nair, N. Balasundaram, and T. Mohapatra. 2003. Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46: 394–403.

    Article  CAS  PubMed  Google Scholar 

  • Singh, K. 1973. Hot air therapy against red rot of sugarcane. Plant Disease Report 57: 220–222.

    Google Scholar 

  • Singh, R.K., J. Singh, M.S. Khan, and H.L. Madhok. 2007. Genetic purity of micropropagated plantlets in Sugarcane using SSR markers National Symposium on Seed Cane, IISR, Lucknow.

  • Singh, R.P., and V.P. Agnihotri. 1987. Thermo-therapy of sugarcane for disease control. In Review of tropical plant pathology, vol. IV, ed. S.P. Raychaudhary, and J.P. Verma, 305–329. New Delhi: Today and Tommarow’s Printers and Publication.

    Google Scholar 

  • Sun, G., M. Bond, H. Nass, R. Martin, and Z. Doung. 2003. RAPD polymorphism in spring wheat cultivars and lines with different level of Fusarium resistance. Theoretical and Applied Genetics 106: 1059–1067.

    Article  CAS  PubMed  Google Scholar 

  • Virupakshi, S., and G.R. Naik. 2008. ISSR analysis of chloroplast and mitochondrial genome can indicate the diversity in sugarcane genotypes for red rot resistance. Sugar Tech 10: 65–70.

    Article  CAS  Google Scholar 

  • Venkatraman, S.T. 1925. Sugarcane breeding in India: hybridization to testing. Agricultural Journal of India 29(3): 173–176.

    Google Scholar 

  • Wei, X., P.A. Jackson, C.L. McIntyre, K.S. Aitken, and B. Croft. 2006. Association between DNA markers and resistance to diseases in sugarcane and effects of population structure. Theoretical and Applied Genetics 114: 155–164.

    Article  CAS  PubMed  Google Scholar 

  • Went, F.A.F.C. 1893. Het Rood Snot. ArchJava Suikerind 1: 243–265.

    Google Scholar 

  • Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395–420.

    Article  Google Scholar 

  • Yadav, R.L. 2006. Research vision to manage red rot disease of sugarcane in India. Sugar Tech 8: 99–100.

    Article  Google Scholar 

  • Yap, I., and R.J. Nelson. 1996. Winboot. A program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMAbased dendrograms. IRRI Discussion paper series no. 14. International Rice Research Institute, Manila, Philippines.

Download references

Acknowledgments

The authors gratefully acknowledge the support and encouragement provided by Dr. R. L. Yadav, Director, IISR, Lucknow.

Author information

Authors and Affiliations

  1. Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow, 226002, Uttar Pradesh, India

    R. K. Singh, M. S. Khan, D. K. Pandey, S. Kumar & S. Lal

  2. Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India

    R. Singh

Authors
  1. R. K. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. S. Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D. K. Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. S. Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. S. Lal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. K. Singh.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Singh, R.K., Khan, M.S., Singh, R. et al. Analysis of Genetic Differentiation and Phylogenetic Relationships among Sugarcane Genotypes Differing in Response to Red Rot. Sugar Tech 13, 137–144 (2011). https://doi.org/10.1007/s12355-011-0076-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12355-011-0076-2

Keywords

Search

Navigation