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Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding

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Abstract

Inter simple sequence repeat (ISSR)-PCR is a technique, which involvesthe use of microsatellite sequences as primers in a polymerase chainreaction to generate multilocus markers. It is a simple and quick methodthat combines most of the advantages of microsatellites (SSRs) andamplified fragment length polymorphism (AFLP) to the universality ofrandom amplified polymorphic DNA (RAPD). ISSR markers are highlypolymorphic and are useful in studies on genetic diversity, phylogeny, genetagging, genome mapping and evolutionary biology. This review providesan overview of the details of the technique and its application in geneticsand plant breeding in a wide range of crop plants.

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References

  • Ajibade, S.R., N.F. Weeden & S.M. Chite, 2000. Inter-simple sequence repeat analysis of genetic relationships in the genus Vigna. Euphytica 111: 47–55.

    Google Scholar 

  • Akagi, H., Y. Yokozeki, A. Inagaki, A. Nakamura & T. Fujimura, 1996. A co-dominant DNA marker closely linked to the rice nuclear restorer gene, Rf-1, identified with inter-SSR fingerprinting. Genome 39: 1205–1209.

    Google Scholar 

  • Arcade, A., F. Anselin, P.F. Rampant, M.C. Lesage, L.E. Paques & D. Prat, 2000. Application of AFLP, RAPD and ISSR markers to genetic mapping of European and Japanese larch. Theor Appl Genet 100: 299–307.

    Google Scholar 

  • Becker, J. & M. Heun, 1995. Mapping of digested and undigested random amplified microsatellite polymorphisms in barley. Genome 38: 991–998.

    Google Scholar 

  • Blair, M.W., O. Panaud & S.R. McCouch, 1999. Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L). Theor Appl Genet 98: 780–792.

    Google Scholar 

  • Charters, Y.M., A. Robertson, M.J. Wilkinson & G. Ramsay, 1996. PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5'-anchored simple sequence repeat (SSR) primers. Theor Appl Genet 92: 442–447.

    Google Scholar 

  • Charters, Y.M. & M.J. Wilkinson, 2000. The use of self-pollinated progenies as ‘in-groups’ for the genetic characterization of cocoa germplasm. Theor Appl Genet 100: 160–166.

    Google Scholar 

  • Chen, Y., G. Hausner, E. Kenaschuk, D. Procunier, P. Dribnenki & G. Penner, 1998. Identification of microspore-derived plants in anther culture of flax (Linum usitatissimum L.) using molecular markers. Plant Cell Reports 18: 44–48.

    Google Scholar 

  • Fang, D.Q., M.L. Roose, R.R. Krueger & C.T. Federici, 1997. Fingerprinting trifoliate orange germplasm accessions with isozymes, RFLPs and inter-simple sequence repeat markers. Theor Appl Genet 95: 211–219.

    Google Scholar 

  • Fang, D.Q & M.L. Roose, 1997. Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95: 408–417.

    Google Scholar 

  • Gilbert, J.E., R.V. Lewis, M.J. Wilkinson & P.D.S. Caligari, 1999. Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theor Appl Genet 98: 1125–1131.

    Google Scholar 

  • Godwin, I.D., E.A.B. Aitken & L.W. Smith, 1997. Application of inter-simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18: 1524–1528.

    Google Scholar 

  • Gupta, M., Y-S. Chyi, J. Romero-Severson & J.L. Owen, 1994. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89: 998–1006.

    Google Scholar 

  • Gupta, P.K. & R.K. Varshney, 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.

    Google Scholar 

  • Hantula, J., M. Dusabenyagasani & R.C. Hamelin, 1996. Random amplified microsatellites (RAMS)-a novel method for characterizing genetic variation within fungi. Eur J for Path 26: 159–166.

    Google Scholar 

  • Huang, J. & S.M. Sun, 2000. Genetic diversity and relationships of sweet potato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat (ISSR) and restriction analysis of chloroplast DNA. Theor Appl Genet 100: 1050–1060.

    Google Scholar 

  • Hussain, A.J., V. Gupta, J. Ali, P.K. Ranjekar & E.A. Siddiq, 2000. Physiological characterization, genetics and molecular mapping of a new source of temperature sensitive genetic male sterility in rice. Fourth International Rice Genetics Symposium, 22- 27 October 2000, IRRI, Philippines, Abstracts p. 95.

    Google Scholar 

  • Joshi, S.P., V.S. Gupta, R.K. Aggarwal, P.K. Ranjekar & D.S. Brar, 2000. Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100: 1311–1320.

    Google Scholar 

  • Kantety, R.V., X.P. Zeng, J.L. Bennetzen & B.E. Zehr, 1995. Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Molecular Breeding 1: 365–373.

    Google Scholar 

  • Kojima, T., T. Nagaoka, K. Noda & Y. Ogihara, 1998. Genetic linkage map of ISSR and RAPD markers in Einkorn wheat in relation to that of RFLP markers. Theor Appl Genet 96: 37–45.

    Google Scholar 

  • Lanham, P.G. & R.M. Brennan, 1998. Characterization of the genetic resources of redcurrant (Ribes rubrum: subg. Ribesia) using anchored microsatellite markers. Theor Appl Genet 96: 917–921.

    Google Scholar 

  • Levin, I.N., E. Gilboa, S. Yeselson, Shen & A.A. Schaffer, 2000. Fgr, a major locus that modulates the fructose to glucose ratio in mature tomato fruits. Theor Appl Genet 100: 256–262.

    Google Scholar 

  • Levinson, G. & G.A. Gutman, 1987. Slipped strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203–221.

    Google Scholar 

  • Lu, J., M.R. Knox, M.J. Ambrose, J.K.M. Brown & T.H.N. Ellis, 1996. Comparative analysis of genetic diversity in pea assessed by RFLP-and PCR-based methods. Theor Appl Genet 93: 1103–1111.

    Google Scholar 

  • Martin, J.P. & M.D. Sanchez-Yelamo, 2000. Genetic relationships among species of the genus Diplotaxis (Brassicaceae) using inter-simple sequence repeat markers. Theor Appl Genet 101: 1234–1241

    Google Scholar 

  • McGregor, C.E., C.A. Lambert, M.M. Greyling, J.H. Louw & L. Warnich, 2000. A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L) germplasm. Euphytica 113: 135–144.

    Google Scholar 

  • Meyer, W., T.G. Mitchell, E.Z. Freedman & R. Vilgays, 1993. Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J Clin Microbiol 31: 2274–2280.

    Google Scholar 

  • Moreno, S., J.P. Martin & J.M. Ortiz, 1998. Inter-simple sequence repeats PCR for characterization of closely related grapevine germplasm. Euphytica 101: 117–125.

    Google Scholar 

  • Nagaoka, T. & Y. Ogihara, 1997. Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor Apppl Genet 94: 597–602.

    Google Scholar 

  • Pasakinskiene, I., C.M. Griffiths, A.J.E. Bettany, V. Paplauskiene, M.W. Humphreys, 2000. Anchored simple-sequence repeats as primers to generate species-specific DNA markers in Lolium and Festuca grasses. Theor Appl Genet 100: 384–390.

    Google Scholar 

  • Prevost, A. & M.J. Wilkinson, 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98: 107–112.

    Google Scholar 

  • Qian, W., S. Ge & D.Y. Hong, 2001. Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor Appl Genet 102: 440–449.

    Google Scholar 

  • Ratnaparkhe, M.B., M. Tekeoglu & F.J. Muehlbauer, 1998. Intersimple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters. Theor Appl Genet 97: 515–519.

    Google Scholar 

  • Reddy, M.P., N. Sarla, C.N. Neeraja & E.A. Siddiq, 2000. Assessing genetic variation among Asian A-genome Oryza species using inter simple sequence repeat (ISSR) polymorphism. Fourth International Rice Genetics Symposium, 22- 27 October 2000, IRRI, Philippines. Abstracts p. 212.

    Google Scholar 

  • Salimath, S.S., A.C. de Oliveira, I.D. Godwin & J.L. Bennetzen, 1995. Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers. Genome 38: 757–763.

    Google Scholar 

  • Sanchez de la Hoz, M.P., J.A. Davila, Y. Loarce & E. Ferrer, 1996. Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley. Genome 39: 112–117.

    Google Scholar 

  • Sankar, A.A. & G.A. Moore, 2001. Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of genetic linkage map. Theor Appl Genet 102: 206–214.

    Google Scholar 

  • Sarla, N., C.N. Neeraja & E.A. Siddiq, 2000. Determining genetic diversity in Indian landraces of rice using inter-simple sequence repeat (ISSR) polymorphism. Fourth International Rice Genetics Symposium, 22- 27 October 2000, IRRI, Philippines. Abstracts p. 217.

    Google Scholar 

  • Staub, J.E., F.C. Serquen & M. Gupta, 1996. Genetic markers, map construction, and their application in plant breeding. HortScience 31(5): 729–739.

    Google Scholar 

  • Tautz, D. & M. Renz, 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12: 4127–4138.

    Google Scholar 

  • Tsumura, Y., K. Ohba & S.H. Strauss, 1996. Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theor Appl Genet 92: 40–45.

    Google Scholar 

  • Varghese, J.P., B. Rudolph, M.I. Uzunova & W. Ecke, 2000. Use of 5'-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L. Theor Appl Genet 101: 115–119.

    Google Scholar 

  • Virk, P.S., J. Zhu, H.J. Newbury, G.J. Bryan, M.T. Jackson & B.V. Ford-Lloyd, 2000. Effectiveness of different classes of molecular marker for classifying and revealing variation in rice (Oryza sativa) germplasm. Euphytica 112: 275–284.

    Google Scholar 

  • Wang, G., R. Mahalingan & H.T. Knap, 1998. (C-A) and (GA) anchored simple sequence repeats (ASSRs) generated polymorphism in soybean, Glycine max (L.) Merr. Theor Appl Genet 96: 1086–1096.

    Google Scholar 

  • Wang, Z., J.L. Weber, G. Zhong & S.D. Tanksely, 1994. Survey of plant short tandem DNA repeats. Theor Appl Genet 88: 1–6.

    Google Scholar 

  • Weising, K., P. Winter, B. Huttel & G. Kahl, 1998. Microsatellite markers for molecular breeding. J Crop Prod 1(1): 113–143.

    Google Scholar 

  • Wolfe, A.D., Q-Y. Xiang & S.R. Kephart, 1998. Diploid hybrid speciation in Penstemon (Scrophulariaceae). Proc Natl Acad Sci USA 95: 5112–5115.

    Google Scholar 

  • Wolff, K., E. Zietkiewicz & H. Hofstra, 1995. Identification of chrysanthemum cultivars and stability of DNA fingerprint patterns. Theor Appl Genet 91: 439–447.

    Google Scholar 

  • Wolff, K. & M. Morgan-Richards, 1998. PCR markers distinguish Plantago major subspecies. Theor Appl Genet 96: 282–286.

    Google Scholar 

  • Wu, K., R. Jones, L. Dannaeberger & P.A. Scolnik, 1994. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res 22: 3257–3258.

    Google Scholar 

  • Yang, W., A.C. de Oliveira, I. Godwin, K. Schertz & J.L. Bennetzen, 1996. Comparison of DNA marker technologies in characterizing plant genome diversity: variability in Chinese sorghums. Crop Sci 36: 1669–1676.

    Google Scholar 

  • Zietkiewicz, E., A. Rafalski & D. Labuda, 1994. Genome fingerprinting by simple sequence repeat (SSR) - anchored polymerase chain reaction amplification. Genomics 20: 176–183.

    Google Scholar 

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Authors and Affiliations

  1. Directorate of Rice Research, Rajendranagar, Hyderabad, 500 030, India

    M. Pradeep Reddy, N. Sarla & E.A. Siddiq

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  1. M. Pradeep Reddy
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  2. N. Sarla
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  3. E.A. Siddiq
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Pradeep Reddy, M., Sarla, N. & Siddiq, E. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128, 9–17 (2002). https://doi.org/10.1023/A:1020691618797

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