I have a very high-level exploratory question about SNPs and comparative genomics.
Lets say I had 2 different populations of the same species and one of those populations was resistant to a particular disease and one of them was susceptible. Naturally I want to try and find out what confers resistance to the healthy population. How would I go about this using SNP data? I appreciate this is a huge question but I'm just trying to find out what areas I need to go and research in more detail.
Lets say I had a full genome sequence for individuals from both populations and knew their SNP alleles. Can the allele frequencies of SNPs in the 2 populations tell me anything? If the allele frequencies of a SNP in the 2 populations differ is that potentially intesting (although it might represent some other difference between the 2 populations other than the disease susceptibility)? How many individuals would i need each population to compare the allele frequencies?
Are there any sorts of statistical analysis I might perform? For example if I found an area of the genome had a higher/lower SNP distribution than the rest of the genome does this tell me anything? For example does a lower SNP distribution mean it is conserved and subject to positive selection? It's been a long time since I studied this so I could be remembering this all wrong.
Many thanks Thanks