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  • ddRAD sequencing for marker discovery

    Hello everyone,

    Seeking suggestion on GBS sequencing. I would like to know what should be the study design for carrying out ddRAD based sequencing of phenotypically distinct lines of insects (say body colour or markings/pattern). The objective is to come up with markers which can distinctively genotype one line from another or molecular barcoding.

    1. If ddRAD can help me achieve what I am thinking ?
    2. How many enzymes or enzyme combinations will be optimum
    3. Which platform will be ideal for this job ?

    Sorry if I am being naive here with the question.

  • #2
    hub_taxa I think that ddRAD sequencing can be a good approach for identifying markers that can differentiate phenotypically distinct lines of insects. But your choice of restriction enzymes or enzyme combinations depends on several factors, including the genome size of your target insect species and the desired level of genomic coverage. You'll need to think about the distribution and frequency of restriction sites within the genome. Using multiple enzymes or enzyme combinations can increase the genomic coverage and the number of markers obtained. I recommend testing different enzyme combinations on a subset of samples to determine the optimal combination for your specific study.

    And your platform choice I would say depends on the depth and throughput you want. Ideally I would say something like a HiSeq or NovaSeq, but you can still get a lot done with a MiSeq if needed. ‚Äč

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