Finding phenotype and genotype associations with GWAS

A powerful application of a variant calling many thousands of SNPs with high-throughput sequencing is genome-wide association studies (GWAS) of genotype and phenotype. GWAS is a genomic analysis of variants in different individuals or genetic lines to see whether any particular variant is associated with a trait. There are numerous techniques for doing this, but all of them rely on gathering data on variants in particular samples and working out each sample’s genotype before cross-referencing with the phenotype in some way. In this recipe, we’ll look at the sophisticated mixed linear model described by Yu et al. in 2006 (Nature Genetics, 38:203-208 ). Describing the workings of the unified mixed linear model is beyond the scope of this recipe, but it is a suitable model for use in data with large samples and broad allelic diversity and can be used on plant and animal data.

Getting ready

In this recipe, we’...