Abstract
In the present study we propose and test the concept of R-ISSR, a new tool for genomic fingerprinting, mapping, and gene tagging. The concept is based on the fact that primers for inter-simple sequence repeat (ISSR) and random-amplified polymorphic DNA (RAPD) analysis elicit different genomic information, and the combined use of these 2 kinds of primers in the same polymerase chain reaction (PCR) reactions might reveal new genomic loci that could not be detected with either technique alone. The feasibility of this tool was first electronically simulated with sequence analysis software andArabidopsis chromosome sequence. Next, different combinations of ISSR and RAPD primers were applied in real PCR reactions to detect new genomic loci in 2 maize lines (Q319 and 1145). Sequencing gels were used to separate PCR products and showed good resolving ability in comparison with agarose gels. RAPD primers could be successfully used with ISSR primers for the detection of new genomic loci and applied in a new way for genomic mapping, fingerprinting, and gene tagging.
Similar content being viewed by others
Abbreviations
- AFLP:
-
amplified fragment length polymorphism
- ISSR:
-
inter-simple sequence repeat
- PCR:
-
polymerase chain reaction
- RAPD:
-
random-amplified polymorphic DNA
- SNP:
-
single nucleotide polymorphism
- SSR:
-
simple sequence repeat
References
Ammiraju JSS, Dholakia BB, Santra DK, Singh H, Lagu MD, Tamhankar SA, Dhaliwal HS, Rao VS, Gupta VS, and Ranjekar PK (2001) Identification of inter simple sequence repeat (ISSR) markers associated with seed size in wheat. Theor Appl Genet 102: 726–732.
Archak S, Gaikwad AB, Gautam D, Rao EVVB, Swamy KRM, and Karihaloo JL (2003) Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome 46: 362–369.
Arens P, Odinot P, van Heusden AW, Lindhout P, and Vosman B (1995) GATA and GACA repeats are not evenly distributed throughout the tomato genome. Genome 38: 84–90.
Blair MW, Panaud O, and McCouch SR (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.
Bornet B, Muller C, Paulus F, and Branchard M (2002) Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var.botrytis L.) Genome 45: 890–896.
Broun P and Tanksley SD (1996) Characterization and genetic mapping of simple repeat sequences in tomato genome. Mol Gen Genet 250: 39–49.
Edwards K, Johnstone C, and Thompson C (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res 19: 1349.
Epplen JT (1988) On simple repeated GATA/GACA sequences in animal genomes: a critical reappraisal. J Hered 79: 409–417.
Kashi Y, King D, and Soller M (1997) Simple sequence repeat as a source of quantitative genetic variation. Trends Genet 13: 74–78.
Lagercrantz U, Ellergren H, and Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21: 1111–1115.
Liu B and Wendel JF (2001) Inter simple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton. Mol Ecol Notes 1: 205–208.
Nandal I, Deubelbeiss C, Guttenbach M, Epplan JT, and Schmid M (1990) Heterogeneities in the distribution of (GACA)/simple repeats in the karyotypes of primates and mouse. Hum Genet 85: 187–194.
Powell W, Orozco-Castillo C, Chalmers KJ, Provan J, and Waugh R (1995) Polymerase chain reaction-based assays for the characterization of plant genetic resources. Electrophoresis 16: 1726–1730.
Ratnaparkhe MB, Tekeoglu M, and Muehlbauer FJ (1998) Inter simple sequence repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters. Theor Appl Genet 97: 515–519.
Sambrook J and Russell DW (1989) Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Tautz D and Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12: 4127–4137.
Terauchi R and Kahl G (2000) Rapid isolation of promoter sequences by TAIL-PCR: the 5′-flanking regions of Paland Pgigenes from yams (Dioscorea). Mol Gen Genet 263: 554–560.
Williams JGK, Hanafey MK, Rafalski JA, and Tingey SV. (1993) Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology 218: 704–740.
Xu SB, Tao YF, Yang ZQ, and Chu JY (2002) A simple and rapid method used for silver staining and gel preservation. Hereditas (Beijing) 24: 338–336.
Yu YG, Saghai Maroof MA, and Buss GR (1996) Divergence and allelomorphic relationship of a soybean virus resistance gene based on tightly linked DNA microsatellite and RFLP markers. Theor Appl Genet 92: 64–69.
Zietkiewicz E, Rafalski A, and Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Ye, C., Yu, Z., Kong, F. et al. R-ISSR as a new tool for genomic fingerprinting, mapping, and gene tagging. Plant Mol Biol Rep 23, 167–177 (2005). https://doi.org/10.1007/BF02772707
Issue Date:
DOI: https://doi.org/10.1007/BF02772707