RAPD-SCAR Markers: An Interface Tool for Authentication of Traits

Abstract

The versatility of the PCR technique is that several kinds of primers can be explored for genome analysis depending on the purpose of study. The easy to access and low cost PCR-based markers include Random Amplified Polymorphic DNA (RAPD). The RAPD markers are easy to develop but lack of reproducibility makes it less reliable and obstacles to their further use in authentication of traits. In addition, other PCR and non PCR based markers like Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Restriction Fragment Length Polymorphism (RFLP) are also employed in authentication of traits with certain restrictions vis-à-vis use of radioactive materials, high cost and requirement of sequence information etc. Therefore, this problem can be overcome by converting RAPD markers to more robust sequence characterized amplified regions i.e. SCAR markers. SCARs are locus specific, co-dominant in nature and amplified by PCR using specific 15-30 bp DNA fragments. For developing SCAR markers, primers are designed from the nucleotide sequences of a cloned RAPD fragments linked to a trait of interest. SCAR markers are easy to develop and reliable tools for DNA fingerprinting. This mini review is an attempt to summarize efficacy of RAPD-SCAR interface in authentication of traits.

DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing

“…SCAR markers are more specific and more reproducible as compared to RAPD [77]. SCAR markers are co-dominant and mono-locus markers and are mostly applied for physical mapping [78]. The procedure for the development of SCAR markers includes purification of PCR fragments followed by designing of SCAR primer [76][77][78][79].…”

“…SCAR markers are co-dominant and mono-locus markers and are mostly applied for physical mapping [78]. The procedure for the development of SCAR markers includes purification of PCR fragments followed by designing of SCAR primer [76][77][78][79]. Polymorphic bands are detected by using agarose gel and then the nucleotide sequence of the selected fragment of DNA is investigated.…”

“…Analysis of the sequence of this polymorphic DNA is made by comparing it with the known DNA sequences available at the NCBI (National Center for Biotechnology Information) database for sequence uniqueness. Then this nucleotide sequence of polymorphic DNA is utilized for the synthesis of specifics SCAR primers [78].…”

Differentiating Authentic Adenophorae Radix from Its Adulterants in Commercially-Processed Samples Using Multiplexed ITS Sequence-Based SCAR Markers

“…Plant DNA barcoding led to remarkable improvements in the identification of the botanical origins of herbal materials and in the quality control of herbal medicines, but it still cannot be applied to many plant taxa because of failed PCR amplification, insufficient sequence variability between species, and incomplete sequence information [1,16,19]. To overcome these limits, the comparative analysis of genomic polymorphisms, using methods such as RAPD and AFLP, and the investigation of new DNA barcode regions using plastid genome sequencing have been conducted for a large number of medicinal plant species [15,24,32]. SCAR markers and multiplexed SCAR marker assays, developed using sequence information from genomic analyses, as well as from DNA barcodes, have become popular because the assays are simple to perform and have low analytical cost.…”

“…A sequence-characterized amplified region (SCAR) marker assay can reliably and reproducibly distinguish species based on sequence information obtained from DNA fingerprinting or barcoding in diverse plants and herbal medicines. This method amplifies only target-containing samples using specific primers and differentiates positive or negative amplification of target regions, as well as length polymorphisms of target regions by gel electrophoresis of closely related samples [22][23][24]. Therefore, the SCAR method is simple to carry out, its results are simple to interpret, and it produces fewer errors in PCR amplification and sequencing [21].…”