Dear  Gregor

I would assume that you would also be interested in identifying the SNP markers.  The best thing to start with is from dbSNP in NCBI GenBank.  Have a match of how many of the SNPs with the traits ( as markers). 

Syntenic mapping could be best done with one go using R based tools. If not Plant USDA and Gramene databases provide you an option.  From the SNPs that match from your first step, query them in other organisms fro comparative analyses: http://archive.gramene.org/db/diversity/snp_query

The SNP to Plant GO could then be used. 

Hope this helps

Prash 

Hi Prashanth

Thank you for your reply. SNP marker were generated from Medicago trunctula

and this is legume model

I see, the GBrowse has an option for you to find syntenies: http://www.medicagohapmap.org/fgb2/gbrowse/mt30/

Hi Parshanth

Thank you for your link, but I am still not able to know how I deal with it. Do you have experience in getting info. from website?. for instance, marker  Mt3g086600

Dear  Gregor

I think the links I sent you could be searched.  Please check this : http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=132

It is being linkedout to http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3880

Now what I don't understand is  you are searching the marker wise, Please try searching SNP data and map them.

Best

Prash  

Thank you for your patient. Let me to tell you what I need in more detail. Unfortunately, I do not have experience about synteny. I have some significant SNP markers associated with some yield traits in Lentil and I need to know if there is a way to find out whether the allele of these marker involved in gene and if it is , what is the function of this gene. The maker Mt3g086600 is bialleleic for two Allele (in my population) which are G:T. G is associated with more than one trait in Lentil.  Here, I want to know if this marker or its allele involved in a gene or not.... correct me please if i am wrong??

Thanks in advance

Certainly, but it looks to me that the marker information is wrong. 

What are those traits?  For example if you want to find genetic variation wrt shoor or root or lentils, you can search those trait-related genes and markers associated with them.  

Did you try the previous link?

When I search Gramene, there are a couple: http://archive.gramene.org/db/ontology/search?id=GR_tax:071622