What is the Difference Between SSR and ISSR Markers

The main difference between SSR and ISSR markers is that SSR markers are microsatellites, whereas ISSR is the genomic DNA between microsatellites.

SSR (Simple sequence repeats) and ISSR (inter-simple sequence repeats) are two types of DNA markers that occur in the microsatellite regions. Microsatellites are a type of VNTR (variable number of tandem repeats).   

Key Areas Covered

1. What are SSR Markers
     – Definition, Structure, Function
2. What are ISSR Markers
     – Definition, Structure, Function
3. Similarities – SSR and ISSR Markers
     – Outline of Common Features
4. Difference Between SSR and ISSR Markers
     – Comparison of Key Differences

Key Terms

ISSR Markers, SSR Markers

What are SSR Markers

SSR markers are molecular markers that analyze DNA regions with 1-6 nucleotide repeats. Therefore, SSR markers are a type of microsatellite DNA, which are a type of VNTR. The main importance of the analysis of SSR markers is the genetic structuration. SSR markers analyze codominant characteristics. Therefore, SSR markers allow identifying heterozygous loci. In addition, these markers allow the identification of multiallelic nature, simultaneous identification of several alleles, reproducibility, high polymorphism, and the uniform distribution of the genome.

Figure 1: STR Markers

Furthermore, the nucleotide sequences of the SSR markers amplify tandem nucleotide repetitions. Microsatellites are DNA motifs with repeating nucleotide sequences. They occur thousands of times in the genome. The two types of microsatellite DNA are short tandem repeats (STRs) and simple sequence repeats (SSRs).

What are ISSR Markers

ISSR markers are another type of DNA marker that contains dominant DNA sequences. The repeats are about 100-300 nucleotides long. ISSR markers are amplified by using primers that anneal to the complementary sequences of two neighboring microsatellite regions in the genome. Therefore, it allows the analysis of multiple loci in a single experiment. However, ISSR markers occur between two microsatellite repetitive sequences. Therefore, ISSR markers allow the amplification of random DNA sequences in the genome.

Figure 2: SSR Markers

Since ISSR markers are dominant DNA sequences, only the presence or absence of DNA sequences can be checked.  DNA markers are important for the identification of genetic variations in breeds.

Similarities Between SSR and ISSR Markers

• SSR and ISSR markers are two types of DNA that occur in the microsatellite regions.
• They are important as genetic markers to identify and characterize populations through nucleotide sequences.
• They contribute to genetic variability.
• Both can be amplified by PCR.

Difference Between SSR and ISSR Markers

Definition

SSR markers refer to the microsatellites, which are a type of repetitive DNA sequence ubiquitous in most plant genomes, while ISSR markers refer to DNA fragments of about 100-3000 bp located between adjacent, oppositely oriented microsatellite regions.

Significance

SSR markers are microsatellite DNA, while ISSR markers occur between microsatellite DNA.

Nucleotide Repeats

While SSR markers contain nucleotide repeats of 1-6 nucleotides, ISSR markers contain nucleotide repeats of 100-300 nucleotides.

Identification of Loci

SSR markers recognize heterozygous loci, while ISSR markers recognize multiple loci.

Amplification

SSR markers amplify tandem repeats, while ISSR markers amplify random sequences of the genome.

Dominance

Moreover, SSR markers are codominant DNA sequences, but ISSR markers are dominant DNA sequences.

Conclusion

In brief, The SSR and ISSR markers are two types of genetic markers important for the characterization of populations. The SSR markers occur in the microsatellites, and they have 1-6 nucleotide repeats. They identify heterozygous loci by amplifying tandem repeats. On the other hand, ISSR markers are the genomic DNA sequences that occur between microsatellite DNA. They are longer repeats of 100-300 nucleotides long. ISSR markers allow the analysis of multiple loci in a single experiment. In addition, they amplify random sequences of the genome. Therefore, the main difference between SSR and ISSR markers is the type of repeats.

References:

1. Silva Junior, M. S. F. S. da, Borges, A. A. de S., Santos, S. R. N., Moura, V. G. de, Silvana, G. R. da, Dias, A. C. S., Araujo, A. M. de, & Filho, J. W. G. de O. (2020, June 5). SSR and ISSR markers in assessing genetic diversity in gallus gallus domesticus: A quantitative analysis of scientific production. Ciência Rural. 

Image Courtesy:

1. “Str profile” By ParinoidMarvin – Own work (CC-BY SA 3.0) via Commons Wikimedia
2. “PAGE AgStain Microsat” By Sekiyu – Own Work (CC-BY SA 3.0) via Commons Wikimedia