Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD

The availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative genomics has proven itself to be an invaluable approach for the systematic, genome-wide identification of conserved non-protein-coding elements (CNEs). However, for many non-mammalian model species, including chicken, our capability to interpret the functional importance of variants overlapping CNEs has been limited by current genomic annotations, which rely on a single information type (e.g. conservation). We here studied CNEs in chicken using a combination of population genomics and comparative genomics. To investigate the functional importance of variants found in CNEs we develop a ch(icken) Combined Annotation-Dependent Depletion (chCADD) model, a variant effect prediction tool first introduced for humans and later on for mouse and pig. We show that 73 Mb of the chicken genome has been conserved across more than 280 million years of vertebrate evolution. The vast majority of the conserved elements are in non-protein-coding regions, which display SNP densities and allele frequency distributions characteristic of genomic regions constrained by purifying selection. By annotating SNPs with the chCADD score we are able to pinpoint specific subregions of the CNEs to be of higher functional importance, as supported by SNPs found in these subregions are associated with known disease genes in humans, mice, and rats. Taken together, our findings indicate that CNEs harbor variants of functional significance that should be object of further investigation along with protein-coding mutations. We therefore anticipate chCADD to be of great use to the scientific community and breeding companies in future functional studies in chicken. Author summary Chickens are raised worldwide as a livestock species to provide us with their eggs and meat, but besides their huge economical impact their genome remains poorly understood. Here we introduce a variant prioritization tool modeled after the Combined Annotation Dependent Depletion (CADD). CADD is a well-established approach to prioritize variants with respect to their deleteriousness for the interpretation of genetic variation that can substantially impact human phenotypes, such as diseases. We applied the CADD approach to chicken (chCADD) to investigate the functional importance of conserved non-protein-coding elements. The chCADD model assigns a score to all possible variation in the chicken genome, which can be used to prioritize genetic variants to be used in for breedings strategies. We used these scores to identify subregions within conserved non-protein-coding elements of relative higher importance. The chCADD score and the identified subregions are expected to support our efforts to pinpoint causal genomic variation throughout the chicken genome.