Abstract
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated.
Highlights
In recent years, many promising new alternative molecular marker techniques have been developed in plant genetics, largely due to rapid growth in genomic research initiating a trend away from random DNA markers towards genetargeted functional markers [1]
Some recently developed techniques can be regarded as under-utilized tools for researchers, and as yet none have become as popular as RAPD or amplified fragment length polymorphism (AFLP), despite the fact that they have been shown to be as or more effective than these traditional techniques
A major disadvantage of some recently developed methods is the need for preliminary genomic information, which in some cases requires additional and time-consuming laboratory work
Summary
Many promising new alternative molecular marker techniques have been developed in plant genetics, largely due to rapid growth in genomic research initiating a trend away from random DNA markers towards genetargeted functional markers [1]. Amplified DNA markers (AADs) Before describing recent developments, some aspects of the first PCR-based methods must be discussed Techniques in this group use genetic markers that occur at multiple sites throughout the genome, banding patterns are a product of amplification from multiple priming sites. When functionality and the resolution provided by slowly evolving DNA regions or fast evolution of SSRs is a problem, conserved DNA or gene family based markers may be good choices Markers belonging to this family can be regarded as a special group of gene-targeted markers (GTMs), which utilize length polymorphisms of exonintron structures in different widely distributed and common plant genes or gene families.
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