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Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?

I think that in the past recombination-based genetic maps were used as blueprints for sequencing projects. But since now the entire genome can be sequenced pretty cheaply both in time and money, what is the unique value of recombination-based genetic mapping?

One thing that comes to mind but I am not very sure. It might be suitable for mapping novel phenotypic markers e.g., unmapped diseases.

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A couple of months ago I listened to a plant physiologist who strongly recommended recombination-based mapping over sequencing based mapping. The main reason he gave was the error-rate of 2nd generation sequencing. The error rate on Illumina platforms are about 1 % if I recall. In a small genome like that of Arabidopsis thaliana (157 Mbp) that accounts for over 1 million sequencing errors. That can of course be reduced having a proper sequencing depth and using the consensus sequence. But it can still cause problems if you're tracking a phenotype caused by an SNV. In plants like A. thaliana where back crossing can be used to create homozygous plants, recombination-based techniques can be particularily effective.

But he was talking from a plant physiologist's view when working with A. thaliana as a model organism. When working with humans which always are heterozygous, can't be back-crossed, don't have a generation time of six weeks and where samples sizes will probably be small I imagine that the situation is different. The classic geneticists' working with human diseases that I have talked have expressed fear that their work will soon be obsolete due to falling sequencing prices and growing sequence data collections.

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