5.2. Simple sequence repeats (SSRs) or microsatellites are DNA stretches consisting of short, tandemly repeated di-, tri-, tetra-or penta-nucleotide motifs. Simple sequence repeats have been found in all eukaryotic species that were scrutinized for them (Tautz and Renz, 1984).
What are SSR markers used for?
SSRs have been the most widely used markers for genotyping plants over the past 20 years because they are highly informative, codominant, multi-allele genetic markers that are experimentally reproducible and transferable among related species (Mason, 2015).
What function do repetitive base sequences have in DNA?
Most of the sequences in this class are located in the heterochromatin regions of the centromeres or telomeres of the chromosomes. Highly repetitive sequences interacting with specific proteins are involved in organizing chromosome pairing during meiosis and recombination.
What do microsatellites tell us?
Microsatellites provide data suitable for phylogeographic studies that seek to explain the concordant biogeographic and genetic histories of the floras and faunas of large-scale regions. They are also useful for fine-scale phylogenies — up to the level of closely related species.
What is SSR in genome?
Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic and abundant sequences dispersed throughout most eukaryotic genomes (1). As co-dominant, locus-specific markers they are widely used for DNA fingerprinting, paternity testing, linkage map construction and population genetic studies (2–4).
Why is SSR a good DNA variant for DNA fingerprinting?
Among several marker types, simple sequence repeats (SSR) or microsatellite markers are considered a desirable tool for DNA fingerprinting and genetic diversity studies, owing to their many advantages including codominant Mendelian inheritance, high polymorphism, and rapid and convenient detection , , , , [ …
What is SSR markers and their types?
The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions …
What is SSR analysis?
Simple sequence repeats (SSR) – also known as microsatellites – have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques.
What is the difference between SSR and str?
STRs, also commonly known as SSRs (simple sequence repeats) or microsatellites, are short repetitive elements of 2–6 base pairs (bp) of DNA sequences (e.g. CATCATCATCAT) abundantly distributed throughout genomes.
What is the significance of repetitive sequence?
Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as “tuning knobs” in the evolution.
Does repetitive DNA influence gene expression?
Furthermore, distinct repetitive DNA promoter profiles are correlated with tissue-specific patterns of expression. These observations indicate that repetitive DNA elements mediate chromatin accessibility in proximal promoter regions and the repeat content of promoters is relevant to both gene expression and function.
What types of repetitive sequences are present in the human genome?
Repetitive DNA can be divided into two classes: the tandem repetitive sequences (known as satellite DNA) and the interspersed repeats.
Are microsatellites coding DNA?
Definition. Microsatellite, as related to genomics, refers to a short segment of DNA, usually one to six or more base pairs in length, that is repeated multiple times in succession at a particular genomic location. These DNA sequences are typically non-coding.
What are microsatellites used for in genetics?
Microsatellites are used for assessing chromosomal DNA deletions in cancer diagnosis. Microsatellites are widely used for DNA profiling, also known as “genetic fingerprinting”, of crime stains (in forensics) and of tissues (in transplant patients).
How is microsatellite used in DNA typing?
Microsatellites or STRs are repetitive co-dominant sequences of 2–6 bp of DNA that are present throughout the entire genome. They are often used for identification or fingerprinting of DNA. Microsatellites are amplified by PCR using fluorescently labeled primers and the amplicons are separated using CE.
What is SSR polymorphism?
SSRs are very polymorphic due to the high mutation rate affecting the number of repeat units and have several advantages over other molecular markers: they allow the identification of multiple alleles at single locus, are equally distributed all over the genome, show a co-dominant inheritance pattern and could be …
What is SSR PCR?
Simple sequence repeat anchored polymerase chain reaction amplification (SSR-PCR) is a genetic typing technique based on primers anchored at the 5′ or 3′ ends of microsatellites, at high primer annealing temperatures.
What is SSR fingerprinting?
Inter-SSR PCR provides a novel fingerprinting approach applicable for taxonomic and phylogenetic comparisons and as a mapping tool in a wide range of organisms. This application of (CA)n repeats may be extended to different microsatellites and other common dispersed elements.
What markers are used in DNA fingerprinting?
Here we present a comparative study of the three marker systems (SSR, AFLP and SAMPL) with regard to their application as DNA-fingerprinting technique. Predominantly the geno- types from G. hirsutum and G. barbadense were con- sidered, as these are the most widely used species.
What is DNA fingerprinting explain?
DNA fingerprinting is a laboratory technique used to determine the probable identity of a person based on the nucleotide sequences of certain regions of human DNA that are unique to individuals.
What is the difference between SSR and ISSR markers?
SSR markers showed a mean PIC value of 0.78 hence the best marker. As RAPD and ISSR markers are biallelic in nature, they can have maximum of 0.50 PIC value. But SSR markers are multi-allelic and their PIC values will be ranging from 0 if it is monomorphic to 1 if it is highly discriminative.
Why are SSRs used in forensics?
Owing to high levels of polymorphism in the repeat lengths between different species and individuals, and functional genetic characteristics, SSRs have been popularly used as genetic markers for artificial trait selection and forensic applications.
Where are short tandem repeats found?
Short tandem repeats (STRs), also known as microsatellites or simple sequence repeats, are shorl tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp (1), forming series with lengths of up to 100 nucleotides (nt). STRs are widely found in prokaryotes and eukaryotes, including humans.
What is SSR markers PPT?
Research Scientist. Microsatellite are powerful DNA markers for quantifying genetic variations within & between populations of a species, also called as STR, SSR, VNTR. Tandemly repeated DNA sequences with the repeat/size of 1 – 6 bases repeated several times.
What type of DNA is extracted for STR analysis?
STR analysis is a tool in forensic analysis that evaluates specific STR regions found on nuclear DNA. The variable (polymorphic) nature of the STR regions that are analyzed for forensic testing intensifies the discrimination between one DNA profile and another.