Genetic mapping of mutations in model systems has facilitated the identification of genes contributing to fundamental biological processes. Using the whole-genome sequencing against pooled members of F2 population is now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds.
But, this in the case of recessive mutants which all individuals are expressing the homozygous for the mutant genome at the locus responsible for the phenotype.
However, such approache is not entirely easy for the characterization of a variety of more challenging mutations, such as dominant.
So that, I'm looking for the best method that allows me to isolate the dominant and homozygous candidates to obtained the DNA pooled for sequencing.
Dominant/recessive or Homozygous/heterozygous are terms used in genetics but they does not exist in the sequencing data or sequence data analysis per se. It is you who will decide what is homozygous et cetera in the sequence analysis. If you have the reference sequence, I would say homology search would tell you the information about your sequence and there are several method which you can find in public domain to analyse SNPs.
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