GBS or RAD?
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4.1 years ago
mahnazkiani ▴ 50

I am interested in using either RAD or GBS method to find the variations between 1 population of susceptible insect and 3 population of resistant insect. The insect genome has not sequenced yet, but I assume that the genome size would be about 400-500 MB. How many samples from each population I need to get? Can I get individual insect from each colony and consider it as a sample or all samples need to have different genotypes? Is there any advantage for either of these methods?

sequencing SNP genome • 1.8k views
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This question has been asked and answered a number of times, e.g.:

RAD-Seq vs genotyping by sequencing

GBS vs RAD

GBS and RADseq

Short (and possibly incorrect) answer: you need a lot of individuals from each population.

Longer (and possibly better) answer: are these "populations" wild populations, or laboratory established populations? For how long have they been kept in the lab? Is there migration between the populations? You need to answer these questions for a proper experimental design.

In my experience, frequently resistant and susceptible lines have been isolated for a while, so they accumulated lots of variants unrelated to resistance. A better approach wold be design some sort of crossing scheme that creates a parental population from the admixture of resistant and susceptible lines, then segregating sub-populations, then genotype and phenotype those sub-populations. The literature on this field is quite extensive.

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Thank you for your response. Populations have been established from the wild populations 3 years before and increased and kept in the separated cages in the greenhouse. We don't expect migration between populations. Do you still think that we need to go to crossing before doing genotyping?

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