Variety Specific Primers
Variety Specific Primers - Related Videos
10:17
Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers
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Cited by 7 •
2017
Most common gut content analyses of macroinvertebrates are visual. Requiring intense knowledge about morphological diversity of prey organisms, they miss soft bodied prey and, due to strong comminution of prey, are nearly impossible for some organisms, including amphipods. We provide detailed, novel genetic approaches for macroinvertebrate prey identification in the diet of amphipods.
11:14
Primer-Free Aptamer Selection Using A Random DNA Library
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Cited by 20 •
2010
SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere with the selection process (false positives and negatives). Here we present a primer-free protocol.
12:01
A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica
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Cited by 5 •
2012
We provide a cost-effective and rapid molecular genotyping protocol that employs variety-specific PCR primers that target DNA sequence differences within the chloroplast trnL-F spacer region to differentiate between varieties of Imperata cylindrica (cogongrass) that cannot be distinguished by morphology alone. These varieties include the federally listed noxious weed, cogongrass and closely-related, wide-spread ornamental variety, I. cylindrica var. koenigii (Japanese blood grass).
15:28
Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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Cited by 41 •
2009
We present a method of targeted ancient DNA sequence retrieval, which we used to reconstruct the complete mitochondrial genomes of five Neandertal individuals. Comparison of these sequences with present day humans suggests that Neandertals had a long term low effective population size.
06:33
A Versatile Pipeline for Analyzing Dynamic Changes in Nuclear Bodies in a Variety of Cell Types
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2024
This method describes an immunofluorescence protocol and quantification pipeline for evaluating protein distribution with varied nuclear organization patterns in human T lymphocytes. This protocol provides step-by-step guidance, starting from sample preparation and continuing through the execution of semi-automated analysis in Fiji, concluding with data handling by a Google Colab notebook.
FAQs
The key design principle is complementarity to a sequence that differs between varieties. When the target sequence is present, the primer can bind and support amplification during PCR; when that distinguishing sequence is absent or sufficiently different, the expected product is not selectively generated. This sequence-level selectivity allows closely related crop cultivars or plant lines to be separated.
PCR conditions determine whether the primer discriminates reliably. Denaturation separates the DNA strands, annealing provides the stage for sequence-specific primer binding, and extension copies the region from the bound primer. Repeating these steps enriches the selected fragment, so the final signal reflects amplification of the targeted variety-associated sequence rather than an unamplified mixture of DNA.
Their value is greatest for closely related varieties because the assay focuses on a difference at a specific DNA sequence. A primer directed at that sequence can provide a molecular distinction even when materials belong to the same crop or biological group. The approach therefore supports more precise variety-level identification than a broad classification alone.
A basic workflow begins with a biological DNA sample and the selected primers, followed by PCR cycling through denaturation, annealing, and extension. The amplified material is then assessed by gel electrophoresis or another detection method. A variety-associated product provides the readout used to compare the sample with expected variety patterns, making the workflow suitable for identification and authentication.
Seed and material authentication are direct applications of these assays. By checking whether samples produce the expected variety-associated amplification pattern, researchers can verify identity and detect unwanted material in a biological collection. The same logic supports genetic purity testing, where the assay helps evaluate whether material remains consistent with the intended variety. These uses are especially relevant when maintaining dependable seed or plant resources.
In marker-assisted breeding, the primers can help track desirable traits through breeding populations by providing a DNA-based marker associated with a variety or line. This allows researchers to follow the presence of relevant genetic material while selecting plants. The resulting information links variety-level genetic identification with decisions about which materials to retain or examine further.