There are a number of molecular markers such as RAPD, RFLP etc.. Why are SSR markers gaining popularity and attention as the markers of choice?
Dear Tanushree
Each marker technique has its own advantages and disadvantages. RAPD markers are very quick and easy to develop (because of the arbitrary sequence of the primers) but lack reproducibility. AFLP has medium reproducibility but is labor intensive and has high operational and development costs. Microsatellites are specific and highly polymorphous, but they require knowledge of the genomic sequence to design specific primers and, thus, are limited primarily to economically important species. SSRs are co-dominant molecular markers that distinguish homozygotic and hetrozygotic individuals and also possess a large number of alleles.
One of the most important characteristic of SSR markers is their reproducibility, which allow to compare results among labs, even among different species. As Seied said, the reproducibility of some of the other techniques mentioned, is reduced, even using the same conditions after each repetition.
Dear Tanushree
SSR markers are gaining popularity among researchers mainly because of their high reproduciblity , co-dominant nature, highly polymorphic nature and because of high number of alleles per locus.
Which means that you can identify small bp variation, which is used to study genetic diversity and can be used as a tool for plant breeding.
Dear Tanushree
Agree with all the above answers and as they have said every techniques has its own advantages and disadvantages. But for marker selection one important criteria is the nature I.e. dominant or co-dominant and SSR is a co-dominant marker which is one of the advantage. Another advantage is that ist is also called as microsatellite marker which is highly variable region of the DNA and hence it easily identify even one bp change. This will help in identifying the genetic relatedness amongst population. Thus it's being used widely over other markers like RAPD, RFLP.
Are codominant markers, reproducibility low cost and highly polymorphism.
It also have a large number of alleles per locus. This means that with a relatively small number of markers 7 (at least), a great diversity of studies, populations, reproductive ecology, conservation, germ-plasm banks, etc. It is important to select markers that segregate independently.
Thank you so much for the content shared here. I particularly wanted to know apart from what's written in theory how practically in lab it's gaining popularity...I got to learn a bit
Tanushree, it's not only theoretical information. If you perform a brief surveing in literature, you'll find a lot of examples regarding the characteristics and importance of SSR markers. I'm working for a private company. The obtention of the genetic profiles of our plus trees (clones/varieties), using SSR markers, isn't of minor importance. Since they'll keep the same allelic patern, in spite of the conditions under they´re growing, microsatellite markers have became in a solid tool for their protection.
Vow Sir... that's something great you shared. I am in the process of reviewing literature actually now. That's great to know how private companies realize the potential of SSR markers as well.
Dear Tanushree,
SSR markers have many advantages over the other marker systems. The first advantage is their high reproducibility, which would be the most important in genetic analysis. Also it does not require template DNA to be ultra pure. The second advantage of the SSR marker system is the polymorphic genetic information contents. The hyper-variable nature of SSRs produces very high allelic variations even among very closely related varieties. The third advantage has to do with the co-dominant nature of SSR polymorphisms. The fourth advantage of the SSR marker system is their abundance and distribution in genomes. As more and more genomic sequences are being identified in various eukaryotic species, it is becoming increasingly evident that SSRs are truly abundant in almost all species, and are well distributed throughout their genomes. Because of these reasons SSR gain more popularity over other marker systems.
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