Coding of the markers for SNP markers where parents have heterozygous condition?

[mukesh choudhary]

Dear Karl,

I am first time handling the SNP data for linkage map construction. 

I have DArT SNP markers where the codes are as: I took female as A and male as B and 

heterozygote as D for coding. For some (~200) markers I have SNP data for male and female as:

Case 1: Female    Male       F2 progenies 

                  0                2         2    2    2    1    2    0    2    2    2    0

I assume that it should be a case of AA (0) x AB (2)..so it should give AA or AB i.e. case of not BB coded as D in read.cross() function. But why I am getting 1 in progenies. Should I code 1 as BB and AB as D for progenies to proceed with markers?  

Case 2: Female    Male       F2 progenies 

                  1               2          0    2    1    2    2    0    2    2    0    1

I assume that it should be a case of AA (0) x AB (2)..so it should give AA or AB i.e. case of not BB coded as D in read.cross() function. But why I am getting 0 in progenies. Should I code 0 as BB and AB as D for progenies to proceed with markers?  

Case 3: Female    Male       F2 progenies 

                  2               0          1    0    1    2    0    1    2    2    0    2

I assume that it should be a case of AB (2) x BB (0) .so it should give BB or AB i.e. case of not AA coded as C in read.cross()- function. But why I am getting 1 in progenies. Should I code 1 as AA and AB as C for progenies to proceed with markers  

Case 4: Female    Male       F2 progenies 

                  2               1          2    2    0    0    1    1    1    1    1    2    -

I assume that it should be a case of AB (2) x BB (1)..so it should give BB or AB i.e. case of not AA coded as C in read.cross()- function. But why I am getting 0 in progenies. Should I code 1 as AA and AB as C for progenies to proceed with markers  

Please help me to understand this situation so, I can use such markers to make a relatively denser linkage map.

Thanks

[Karl Broman]

I'm sorry, I don't understand the question.

karl

[mukesh choudhary]

Hi Karl

Sorry for making it more complex. I am attaching my datafile.

description: SNP 1 Row Mapping Format: "0" = Reference allele homozygote, "1" = SNP allele homozygote, "2"= heterozygote and "-" = double null/null allele homozygote (absence of fragment with SNP in genomic representation)

Please have a look at the parental calls (GG and GH columns) for markers highlighted in different colours (e.g. row number 685 to 969 in grey colour is case where parent 1 is 0 and parent 2 is 2; each different colour is a separate kind of case as asked in the question).

I want to know how I can use such highlighted markers by proper coding.

Thanks

Best Regards

Mukesh Choudhary

Scientist- Senior Scale (Genetics and Plant Breeding)

ICAR-Indian Institute of Maize Research, PAU campus, Ludhiana-141001

(Ministry of Agriculture and Farmer's Welfare, GoI)

Mobile: +91-9560439868; e-mail: (P) mukesh.c...@yahoo.com

(O)- mukesh.c...@icar.gov.in

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[Karl Broman]

R/qtl is developed for crosses between inbred lines, and can't handle heterozygosity in the founders.

In an intercross, the founders are homozygous for alternate alleles at a segregating marker, and the F1 are all heterozygous.

I still don't quite understand the nature of your cross, but it doesn't seem like the markers you're asking about can be handled in R/qtl.

karl