Wow nice , concise and great explanation, can u help in answering the question New allele in data base how affects the results of SSP or SSOP, kindly make a video on this emphasising on there differences ....thanks once agaib
I have a doubt. Suppose we have two parents P1 and P2 and we want to confirm that their cross produced a hybrid. So will make SSR primer from both parents or single one??
SSR primers are usually conserved. So same primers can amplify both the parents. The amplified fragment can have SSR length variaition which you can see on gel.
I have a question about the last bit about validating the markers on gel; Each sample has a different number of bands (different sizes) so if you have validating it does this mean that those 13 individuals were testing earlier and now you are cross checking the old data with this one?
We design ssr marker or priner from specific sequence. Once designed you can PCR amplify this marker across different individuals. Each individual may show bands similar or dissimilar in size to the other. Here, 1 ssr marker is amplified in 13 individuals in few individuals it show similar sized bands in others it show different sized. When you analyze data, you score all the bands in every individual. Based on this data you determiner genetic similarity among individuals. Hope this answers your query.
Yes, the flanking region is almost always conserved. but the SSR region is prone to vary. Even in closely related varieties and sometimes acroaa the species SSR flanking regions are conserved. This makes them crosstransferable markers.
Hi Jerry. ISSR are universal primers that work across species. So even of you do not know gene/genome sequence you can use these universal primers. These are like RAPD primers, dominant in nature. Comming to polymorphism, if there is sequence variation in primer binding site you may not get amplicon. hence pesent absent variation will be observed in different individuals. Hope this answers your question.
when u know the locus and able to visualize both the alleles, you can say its codominant marker. if you get band for only one allele or you do not know exact locus/DNA region, its dominant. AFLP produce multiple bands hence refered as dominant. RFLP uses specific probes that bind complementary DNA locus and resolved both the alleles so its codominant.
Based on gene of interest to be studied you can design probes for RFLP. RFLP is challenging because of this and you need to know gene or genome sequence for probe designing. AFLP does not need prior sequence information and bands become visible because of amplification using adapter specific sequnces and PCR. Aflp is easier and cn be done with any plant whether or not gene sequence is available.
