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Application of inter simple sequence repeat (ISSR) markers to plant genetics
Author(s) -
Godwin Ian D.,
Aitken Elisabeth A. B.,
Smith Lawrence W.
Publication year - 1997
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150180906
Subject(s) - microsatellite , biology , genetics , rapd , dna profiling , genetic marker , polymerase chain reaction , genome , primer (cosmetics) , restriction fragment length polymorphism , locus (genetics) , sequence tagged site , genetic diversity , molecular marker , computational biology , dna , gene mapping , allele , population , gene , chemistry , demography , organic chemistry , sociology , chromosome
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) 8 RG or (AGC) 6 TY. 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 32 P or 33 P 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.