If we have one SSR having trinucleotide repeat and another with hexanucleotide repeat, whether this difference in length of repeat motif will affect, in any way, the level or status of polymorphism of that SSR in different individuals?
Can trinucleotide repeat SSR show more polymorphism than that of hexanucleotide repeat SSR or vice versa?
The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. -
Zhao Y, Prakash CS, He G. Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Res Notes. 2012 Jul 20;5:362. doi: 10.1186/1756-0500-5-362. PMID: 22818284; PMCID: PMC3500262.
Shivaji Lavale Long time ago one rice researcher told that SSRs with more than 9 repeats have higher variability compering to shorter SSRs.
@Alex Ignatov It is evident that polymorphism status is getting affected with change in either length of repeat motif or number of repeats.. However it is varying in different species... So there cannot be a hard and fast rule drawn out of this. Isn't It? It may not work for some other species.
This kind of analysis is needed to be done for each plant species so that polymorphism potential of SSRs is predicted and accordingly it is utilised efficiently.
"Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes"
"Genome‑wide characterization of simple sequence repeats in Palmae
genomes"
SSRs show high polymorphism and certainly the length of nucleotide repeat in SSRs affect the level or status of polymorphism of that SSR among different individuals, why not!!! As per the literature available (Duran et al 2013 (attached) SSRs are not common in coding seq. region. By chance if there is any change it effect protein function. This is in case of trinucleotide repeats. Either increase or decrease the amino acid number as well leads to premature frameshift mutation and leads to abruptly truncate the protein. Naturally they subjected to negative selection. It was estimated that SSRs other than trinucleotide in coding region are detrimental in coding sequence and would be less common. Studies shown that SSRs not randomly distributed among UTR and protein coding exons. Variations in 5'UTR control the the expression via transcription slippage could cause the expanded mRNA cause disrupt slicing. Certain species might adapt for fast evolution. SSR alterations in coding regions might be biased synonymous changes.
Jetty Ramadevi " By chance if there is any change it effect protein function. " - There are some data that degenerated SSR can be included into coding seuence at the end of genes.
Yes, Alex, it may happen. Check the following link.
Protein Misfolding and Degenerative Diseases
(https://www.nature.com/scitable/topicpage/protein-misfolding-and-degenerative-diseases-14434929/)
Jetty Ramadevi Rare or not - it is a matter of method used for recognition of degenerated (hidden) SSR within gene sequences. Look at works of E. Korotkov
Chaley MB, Korotkov EV, Skryabin KG. Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples. DNA Research. 1999 Jan 1;6(3):153-63. and more recent: https://scholar.google.ru/citations?user=D8L4kT4AAAAJ&hl=en&oi=sra
Yes, it depends on duplications, nucleotides spatial organisation. Certainly, structure of the gene and protein conformations are interrelated. I need to edit my answer (done).
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