We have 300 RILs which was genotyped with the 35 markers.
A subset of 300 genotype i.e. 92 genotype was analysed for the SNP by GBS.
and We have phenotypic data for all the 300 lines.
How can we build map containing both SNP and SSR markers and use for QTL mapping?
Hi Kashmiri,
it depends on the mapping software and its coding for the diverse markers. But in general you can seperate each SSR marker in all its different alleles and code them as a dominant marker, e.g.:
SSR1_Allel1: 1 0 1 0 0...
SSR1_Allel2: 1 0 1 1 0...
by this you can combine the alleles finally and even calculate whether the are linked in coupling or repulsion etc. if this is intresting for you.
regards
I agree with the suggestion from Stephan Schie , you convert your data in 0/1 format on the basis of SSR allels and then combine with SNP data.
New ICIM v4.2 has SNP data conversion option where you can easily convert your large SNP genotyping data into A, B, H or X format quickly. You read the manual first then use its "testsnp" example file given with it. Then as Vijay Gahlaut sir suggested, combine SNP data with SSR data.
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