Generating genetic map using the mapping population (GBS data)

Question

[arnstrm]

Hi,

I am looking at ways to generate a linkage map from the GBS data. The data comes from the mapping population (F2), but parents are not genotyped. Although I can easily call the SNPs using either Stacks or TasselGBS, I have no clue how can I create a genetic map. Also, genomes for both the parents are available (scaffolds for one parent, chromosomes for the other). Can anybody give me some ideas about how to proceed?

Thanks very much for your time!

[h.mon]

How were the genomes for the parents generated? High / medium coverage whole genome shotgun sequencing? Do you have the original reads used for genome assembly? You could map and genotype the parents if you have these reads. SAMtools has an option to skip unlisted positions (--positions FILE skip unlisted positions (chr pos) or regions (BED)), so you could map the GBS sequencing on the parents, create a bed file with the positions, and call variants only on these positions.

I am sure there are options if you do not have information on the parental lines, but right now I can't think of any. Anyway, some questions: are the parental lines highly inbred? Diploid or polyploid? How many chromosomes? F2 population size?

[DiegoV.O.]

Hi arnstrm,

I have the exact same question, except that I do have GBS data for both parents. Were you able to create a genetic map?

Best regards