The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data

Abstract

The use of dense SNPs to predict the genetic value of an individual for a complex trait is often referred to as “genomic selection” in livestock and crops, but is also relevant to human genetics to predict, for example, complex genetic disease risk. The accuracy of prediction depends on the strength of linkage disequilibrium (LD) between SNPs and causal mutations. If sequence data were used instead of dense SNPs, accuracy should increase because causal mutations are present, but demographic history and longterm negative selection also influence accuracy. We therefore evaluated genomic prediction, using simulated sequence in two contrasting populations: one reducing from an ancestrally large ..