Phenotypic Variation Explained By Snps In Gwas

Question

[kumar.vinod81]

Hi, Can someone please explain what is the mean of phenotypic variation explained by SNPs in GWAS? As much as I know it is the r2 calculated through software using different models in GWAS. But I am confused with some of the words used in tutorials like heritability. So please anyone make me clear about this. I am working on GWAS in a diploid plant species using 5000 SNPs and just want to know the meaning of r2 values. Thanks,

Vinod Kumar

Answer 1

[Genotepes]

Heritability is the proportion if the variance explained by the genetic polymorphisms. There are severalheritabilities and I guess here it is more the additive heritability (also names narrow sense I think, but definitions vary somehow). For a quantitative trait in an unselected population, it can ne related to R2 when you know all the truly associated SNPs (you need to account for the SNPs'variance). Otherwise you need some methods of correlation between genetic identitiy by descent and phenotypic ressemblance for pairs of individuals.

See below a modern version - and in general you may follow the work of Visscher's team (in human genetics, don't know for others).

http://www.sciencedirect.com.gate2.inist.fr/science/article/pii/S0002929711000206