Is Re-Sequencing Of Trait-Associated-Regions Required To Capture The Causal Variant?

Question

[kumar.vinod81]

Suppose I've captured some SNPs which are significant for a trait. Now, I want to know that re-sequencing of these regions are required to capture the actual variant or what are other methods available to know the functional implication of such SNPs on phenotype. Some studies are available in Human but in plant, I've not found any studies on tag SNPs.

Answer 1

[Michael]

I suggest you try a variant effect prediction approach first: Anyone know a *general* variant (SNP/indel) effect predictor / annotator? Also, did you test for deviation from Hardy Wienberg equilibrium: What is the importance of the Hardy Weinberg Equilibrium in GWAS?

What you should do to validate that you found the causal variant or the causal gene depends on the genotyping platform and in which kind of region the variant is located in. So I would like to ask you for more information about the genotyping platform and where the associated SNP is located (in a gene, CDS, etc.) This information also depends on the quality of the genome annotation.

Sanger sequencing of the region has no influence on the significance of the association of the genetic marker, you will be simply more sure that the genotype is not caused by a genotyping error. Also, sequencing the complete CDS can reveal further variants in close proximity which might be causal as well. On the other hand, if your genotyping was done by re-sequencing already, this might not be totally necessary. Also, to do sanger sequencing, I think you should create inbred lines from the plants with and without the phenotype, and sequence the region in both.