Dear all. I am in the process of performing a de novo assembly, and I am wondering if it is possible to create a linkage map without performing controlled experimental crosses (it is logistically impossible for us). Several papers have used whole-genome resequencing of wild individuals in Great Apes to estimate recombination hotspots in the genome using segregating polymorphisms to estimate LD. However, I am wondering if it is possible to also take advantage of this LD information to scaffold draft genome assemblies into chromosomes. I understand that it is impossible to obtain an accurate map distance because the detailed genealogy of the sampled individuals cannot be known for certain, but intuitively this should not affect marker order. Unfortunately most of the map construction programs requires a controlled cross (F2, BC, RIL etc.) as input. I am wondering if any of you knows how to go about this? Thank you!
Hey Rongfeng,
Some details about the focus species would help. What we did for our study species (a frog) was to find mating pairs in the wild, placed them in an enclosure until they laid the egg masses, and then collected tissue samples from both parents and ~150 offspring per mating pair.
Maybe you can reproduce such a design in your focus species?
Hi Lorenzo, thank you for your suggestions. The method you're describing is an F1 mapping cross performed between 2 outbred individuals. Unfortunately we don't have the funding to genotype so many offsprings nor do we have the space to do this cross. We were thinking about using wild populations directly, but from my data it looks like LD between loci drops to baseline within 5kb, which probably will not be useful for scaffolding (given that our longest insert size is 10kb already).
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