Hi, I am working on GWAS for identification of markers and candidate genes associated with leaf rust and powdery mildew resistance. I was reading an old paper and in that paper they identified one QTL associated with leaf rust resistance on long arm of chromosome 2H. They mentioned one SSR marker close to that QTL. Now I was interested to compare that QTL position with my own results because I also identified one QTL on long arm of chromosome 2H.
Is there any way to identify the physical position of that QTL through SSR marker information ??
I will appreciate your response.
Thanks,
Hi Hafiz,
you could blast both of the marker sequences here at the IPK
https://galaxy-web.ipk-gatersleben.de/
Or at the NCBI
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
to locate them on the chromosome.
kind regards
Stephan
Hi, Thank you Stephan Schie
I have BLAST both SNP and SSR markers sequences on NCBI. I am satisfied with the BLAST results of SNP marker and I verified from GrainGenes database (https://wheat.pw.usda.gov/GG3/). However for SSR, the sequence is just few bases long and the BLAST hit showing 100% similarity with hundreds of regions on the same chromosome. ?
I would expect so,
may be you could download (may be for another line/genotype) the contig and reblast it to the reference genome to be sure !?
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