GBS vs skim secquencing

Question

[Betrobert]

Hi, I have 30 NILs samples of Drosophila that were, first, selected for a certain morphological trait and then isogenized. I started with an F1 between two species (A and B) and followed by backcrossing females with males of species B and selected lines showing the phenotype of species A for the trait of interest. Since I have the genomes of both parents. What is better than GBS (reduced genome) or skim secquencing?

[h.mon]

Better in which way? More resolution? Cheaper?

[Betrobert]

You're right, I'd like to know which method will give me more resolution.

[Betrobert]

i need to map the reads onto the genomes of both parentals to identify sequences of species A in the background genome of species B

Answer 1

[Betrobert]

You're right, I'd like to know which method will give me more resolution.

Answer 2

[h.mon]

Have a look at this paper. I think skim sequencing (usually called skimGBS) will provide more markers at a lower cost per marker, but it will cost more per sample.

But I am not sure either method is the ideal for NIL lines. After a few rounds of introgression (how many did you perform), most of the genome should already be from species B. Do you have an idea of the trait architecture? How many genes or regions are involved? Some preliminary mapping information? For example, if you already know the region of interest, you could map by amplicon sequencing.

[Betrobert]

Thanks for your answer! I think I decided on GBS, since my NILs are not completely isogenic, they are still segregating in areas that I do not know, and skimGBS offers very little coverage (2x), which would be a problem, since it could not distinguish a polymorphism from a sequencing error. I haven't idea of the genetic architecture, I don't know how many genes or where they can be, I suspect it is polygenic because it is a quantitative character. It is the first approximation to know a little about it.