hello dear, according to me you are very correct ....SSR marker system is very potent marker system for hybrid purity check, ya if you asking about SRAP : it targets coding sequences in the genome and results in a moderate number of co-dominant markers which having certain limitation and other two marker system ISSR, AFLP quite lower marker in respect off SSR............

hello dear, according to me you are very correct ....SSR marker system is very potent marker system for hybrid purity check, ya if you asking about SRAP : it targets coding sequences in the genome and results in a moderate number of co-dominant markers which having certain limitation and other two marker system ISSR, AFLP quite lower marker in respect off SSR............

Thank your sir,

For responding my question and giving me a useful information..

Ya, you are right sir for this thing I think the SSR markers fits good.I worked this strategy in Tomato and I got fruitful result and even I am continuing in Chili getting good result so far.Now I want to continue the same even in Cucumber and Brinjal and presently I am looking for the marker resources for these. Sir, let me know if you have any resources or information available with you ...

with regards...

I also agree with Anupam...on use of SSR for hybrid purity...Anand if the utility of SSR is good in one crop for hybrid purity..they should be eually useful for other crops too....the only limitation would be how much resources are available in the crops of your interest ...then it may be easy way out.....else if you have to develop the SSRs first...it may take considerable efforts from your side...

@Ajay Saini

Thank you for your response....

Ya, you are absolutely right and you pointed the exact point here regarding the limitation of markers in our interested crop.I am not going to develop any more SSR markers as you said, it will take considerable effort and time too...so right know I am hitting the publicly available resources for markers and try to utilize them if not succeeded then think about the development of more SSR markers.I have one more question here for you..can we fix the number of markers for screening with particular crop to check the hybrid purity?

Dear Anand SSR will be a better choice for testing the purity of Hybrids.

Dear Ananad

SSR is the best choice

Please do not consider marker types but rather to focus on conserved polymorphic exon regions. Species discrimination should be based on stable (these are exons) but conserved (exons again) regions and SNPs would be better choice. Of course you should try all other markers (If found discriminative and conserved).

you won't go wrong with SSRs

SSR is good and accurate technique for hybrid purity test. For more detail please contact with Dr. Aftab Bashir (Principle Scientist; NIBGE). here is his email address

Of those markers listed, SSR is good, but genomic sequence-based SSR markers are the best to use. You may want ot avoid the use of EST-SSR for this particular purpose.

Dear Annad: The best choice is SSR, exist SSR specific for the varietal, if hybrid is diploide you can check the origin of this without any problem, ideal homocygote SSR varietal specific.

Http://www.jstage.jst.go.jp/article/jsbbs/58/4/475/_pdf

SSR or EST-SSR are the best for this purpose

SSR marker will be more specific than the other markers

SSR marker is best one..if the markers are available for particular crop,......

SSR markers will be available for particular crop unless some cross species will work or will not work better go to get particular crop specific markers

SSR marker will be more specific than the other markers releted to hybrid sequence

There are several molecular markers that can used, so SSR will be better for test hybrids purity.

@Esteba Nova...

Thank you for your useful information and suggestions.I will try to make use of your information....

@ All

Thank you friends for your support and suggestions... I will go through your suggestions and will upload the results....

I prefer SSr marker if its PIC (Polymorphic Information Contents) was high.

@Marines Gniech K

Thank you for providing me the details....

1.To fix the number,we need to have more nor of markers but I think we can't limit it.

2. But if we know the parental types and we have around 5-6 robust polymorphic markers between the two parental types we may conclude the limit. I am not sure about this strategy so I will clarify this with experts let us see...

@ Mehdi H

Ya absolutely you are right sir,

1.The PIC value most matters for selecting the markers for screening or to check the Hybrid purity..

2.Even we can use this information for Genetic diversity check also.....

Dear Researcher,

i have glycerol stocks of gene construct pCAMBIA1305.2-AtDREB1a, i want to isolate plasmid DNA very urgently possibly tomorrow itself, People can suggest me to isolate rapid growth of E. coli culture

SSR markers will be more specific compared with other markers

To test for hybrid purity you need a codominant marker system and from the list you posted only SSR are codominant. But SSR must be designed, which make them expensives to desing and if you do not have the information or the sequence available impractical. In the case of AFLP you can create a codominant maker system if you are able to evaluate the band intensity, so in this case you have a third value, but this is impractica too and no very robust. Regarding the number, you need as much as possible, but in any circunstance around 1000 SSR marker, which must be maped across all the chromosomes of the plant you are studing. As an example I was part of the team working on the sequence of the genome of Theobroma cacao var Criollo, the cocoa tree, and the genome sequenced was from a homocigous tree from Belize. This tree was evaluated as highly homocigous using 1100 SSR.

@Diogenes Infante

Thank you sir,for your kind response and giving me suggestions...sir I want to know...

1.1000 to 2000 SSR markers will be used to map on chromosome/linkage groups .These are earlier used to check the parental polymorphism and the polymorphic will be selected,genotype d and mapped on the respective linkage groups.among these 100-200 markers will be mapped.

2.can I pick these polymorphic primers for the purity check?????? and restrict the numbers????

3. If so for these available markers how many lines/plants can I use to check the purity????????

with regards....

@Rachita saxena..

ya you are right....the SNP's are more robust and even useful than the SSR's but these required basic platform, we will try to upload this....yes this will reduce the nor of markers for more no of plants we need to screen as you mentioned...

Well, regarding the number of plants, you need enough to perform basic statistic, so you need at least three samples for each line/plant. Number 2.: Yes, you can check purity with SSR, untill the point or the region you are studing, but yu cannot reduce the number, what it is necessay is to link some markes to the genes you are interested, that is the challenge.

Thank you sir

According to my knowledge, SSR is the best marker system for hybrid purity check and F1 confirmation.

Good luck

based on my knowledge on SSR after use with my colleague in the test of hybrid purity when we were trying to breed cowpea which was resistant to striga, i will recommend SSR for you because the results were very appealing.

Regarding the sources to your SSR markers on the mentioned vegetable above i will recommend that you have a check on KIRK HOUSE they can be of help.

@Jacob J

Thank you for your suggestions and information....Ya you are right that SSRs are robust and they are good enough to test the hybrid purity in any crops.As you mentioned can you provide me the details of KIRK HOUSE, means how and where to approach them?????

This can do you a lot of good ( www.kirkhousetrust.org)

@Jacob

Thank you I will go through it......

SSR marker is good for hybrid purity check.

Dear Dr. Anand A Khot ,

Greetings, thank you for your question.

SSR is the best DNA markers because it is specific for genome, co-dominant, and other advantage for each crop you could get specific SSR. You will get a specific band for each genotype and you could show the differences between genotypes and you could check the purity for your materials.

with best regards

Khaled

Yes Sir,

You are right SSR's are co-dominant and are good to prefer for hybrid purity check...

SSR Markers is best for your study

Yes, SSR is the best choice. The SSR markers are co-dominant and consistent through mitotic cell division.  Their passage through meiosis follows Mendelian genetic roles too. Occurrence of non-designated SSR alleles among cross progenies is very, very rare. See Lu et al. 2015. Genetics and Molecular Research 14(4):18384-18395.

SSR markers best as explained by Dr. Yong-BaoPan