Predictive ability of genomic prediction in layers when including CADD scores as genome function information

Accuracy of genomic prediction is key for genetic progress in breeding programs and including genome functional annotation may help. Here we report on the added value of Combined Annotation Dependent Depletion (CADD) scores to weigh SNPs in GBLUP analyses. Multiple transformations of CADD scores were considered and empirically validated on a layer dataset including 5 traits and 18K animals with 27K SNP genotypes. This initial analysis revealed that the use of (squared) CADD scores yielded marginally higher accuracy for 3 traits. We anticipate that the added value of CADD scores will increase by using a higher number of SNPs and ultimately whole genome sequence SNPs.