Application of inter simple sequence (ISSR) markers to plant genetics

Department of Agriculture, University of Queensland, Brisbane, Australia.
Electrophoresis (Impact Factor: 3.03). 01/1997; 18(9):1524-8. DOI: 10.1002/elps.1150180906
Source: PubMed


Microsatellites or simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Single-locus SSR markers have been developed for a number of species, although there is a major bottleneck in developing SSR markers whereby flanking sequences must be known to design 5'-anchors for polymerase chain reaction (PCR) primers. Inter SSR (ISSR) fingerprinting was developed such that no sequence knowledge was required. Primers based on a repeat sequence, such as (CA)n, can be made with a degenerate 3'-anchor, such as (CA)8RG or (AGC)6TY. The resultant PCR reaction amplifies the sequence between two SSRs, yielding a multilocus marker system useful for fingerprinting, diversity analysis and genome mapping. PCR products are radiolabelled with 32P or 33P via end-labelling or PCR incorporation, and separated on a polyacrylamide sequencing gel prior to autoradiographic visualisation. A typical reaction yields 20-100 bands per lane depending on the species and primer. We have used ISSR fingerprinting in a number of plant species, and report here some results on two important tropical species, sorghum and banana. Previous investigators have demonstrated that ISSR analysis usually detects a higher level of polymorphism than that detected with restriction fragment length polymorphism (RFLP) or random amplified polymorphic DNA (RAPD) analyses. Our data indicate that this is not a result of greater polymorphism genetically, but rather technical reasons related to the detection methodology used for ISSR analysis.

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    • "These regions lie within the microsatellite repeats and offer great potential to determine intra-genomic and inter-genomic diversity compared to other arbitrary primers, since they reveal variation within unique regions of the genome at several loci simultaneously. They exhibit specificity of sequence-tagged-site markers, but need no sequence information for primer synthesis enjoying the advantage of random markers (Zietkiewicz et al., 1994; Goodwin et al., 1997). The primers used in ISSR analysis can be based on any of the SSR motifs (di-, tri-, tetra-or penta-nucleotides) found at microsatellite loci, giving a wide array of possible amplification products, and can be anchored to genomic sequences making either side of the targeted simple sequence repeats (Zietkiewicz et al., 1994). "
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    ABSTRACT: Inter simple sequence repeat (ISSR) analysis, using 14 primers was performed to estimate genetic diversity among 27 landraces of Hassawi rice growing in Al-Ahsa region of Saudi Arabia and deposited at King Abdulaziz City for Science and Technology with KACST IDs. The average polymorphism produced by 11 selected primers was more than 75%. The analysis of ISSR polymorphism divided the examined rice landraces into two groups; In one group (A), one accession (KACST 191) was clearly delimited as a distant landrace from other 12 landraces grouped in two clusters; cluster I of seven landraces of close geographic distributions; four of them grow at close geographic locations (KACST IDs 32, 183, 184, 185, 186, 187 and 188) and cluster II is comprised of five landraces KACST IDs (190, 308, 352, 353 and 355). In group B, the landraces were more closely related to each other as compared to the landraces of group A. In this group a small cluster of two landraces (KACST 305 & KACST 333) was clearly distant from a large group of three clusters comprised of landraces having KACST IDs 189 & 192, landraces 302, 306, 307, 308 & 310 and landraces with KACST IDs 334, 351, 354, 356 & 357 respectively. These results indicate that ISSR fingerprints are efficient in the identification and resolution of genetic diversity between the landraces of the Hassawi rice and will be an efficient method in the authentication of the rice germplasm in the gene bank of Saudi Arabia.
    Preview · Article · Sep 2015 · Saudi Journal of Biological Sciences
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    • "[2] Polymorphic markers based on short DNA sequences reveal genome variations among expressed and non-expressed regions and are quick, reliable and reproducible.[3] Among the different molecular markers, inter simple sequence repeat (ISSR) markers are rapid, cost effective and do not require any sequence information of the genome under study [4] or any radioactive labelling based assay.[5] ISSR-polymerase chain reaction (PCR) analysis involves gene amplification of a region between two inversely oriented microsatellites placed at an amplifiable distance.[2] ISSR markers have been used to resolve polymorphisms among plant accessions by generating a large number of markers that target multiple microsatellite loci distributed across the genome [6] and also among highly related species.[7] "
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    ABSTRACT: Genetic diversity fosters the quintessence of speciation and species acclimatization of plants in their in situ environment. Members of Cucurbitaceae, an edible and economically vital crop family, have spread across the world, dominating the tropical regions. Thus, a study of the genetic relationships among cucurbit cultivars would throw light onto the extent of diversification among these vegetal crops. The present study endeavours to understand the phylogenetic patterns and relatedness among selected species of cucurbits, using inter simple sequence repeat (ISSR) markers, which are quick, reliable and produce sufficient polymorphisms for large-scale DNA fingerprinting purposes. A total of 117 bands, of which 57 were polymorphic, were amplified by five primers. The phylogram generated on the basis of Jacquards’ similarity coefficient revealed a close genetic relationship between C. maderaspatanus and C. melo, while C. sativus, a member of the same genus, was placed as a distant relative from both species, thereby demonstrating remarkable diversification among members of the same genus.
    Full-text · Article · Jul 2015 · Biotechnology & Biotechnological Equipment
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    • "Inter-simple sequence repeat (ISSR) is a PCR-based technique that involves the amplification of DNA sequences between simple sequence repeats (SSR) by means of anchored or non-anchored SSR homologous primers (Zietkiewicz et al. 1994). ISSR does not require information about genome sequence in advance and can detect a greater number of polymorphisms than RFLP or RAPD (Godwin et al. 1997). ISSR is therefore an efficient tool for analysing genetic diversity within closely related species (Yu et al. 2008), and for studying genetic populations of fungi (Menzies et al. 2003; Chadha and Gopalakrishna 2007). "
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    ABSTRACT: Microdochium majus and Microdochium nivale are two of fungal pathogens that cause Fusarium head blight (FHB) in wheat, and have also caused pink snow mold in eastern Hokkaido, Japan. With the aim of assessing levels of genetic variation and population structure, 172 isolates of these Microdochium species obtained from five populations of infected wheat seeds were first classified into each species using polymerase chain reaction (PCR) amplification with specific primers. In total 165 (95.9 % of all isolates) and seven isolates (six of Tokachi populations and one of Abashiri populations) were identified as M. majus and M. nivale, respectively, indicating that M. majus was predominant and the main causal pathogen of FHB in this area. Inter-simple sequence repeat (ISSR) analysis showed that the total genetic diversity was 0.023 when estimated by Nei’s gene diversity index within the five populations dominated by M. majus. An AMOVA analysis also showed that 86.74 % of the total genetic variation was within populations and 13.26 % among populations. These results indicated that little genetic differentiation occurred among the five populations of M. majus. Based on the unweighted pair group method of cluster analysis using the ISSR data, all isolates were identified as one of eight haplotypes in M. majus or six haplotypes in M. nivale, allowing the construction of a dendrogram with two clades corresponding to each species. There was no correlation between the clustering of isolates and their geographic distribution on the tree. These findings show that migration is likely playing an important role in the population biology of M. majus, providing some support for the prediction of epidemics of fungicide resistant strains within populations of the FHB pathogen.
    Full-text · Article · Dec 2014 · European Journal of Plant Pathology
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