Avian Genomics in Animal Breeding and the End of the Model Organism

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

“…Our whole-genome resources are already helping researchers investigating novel transcript sets to distinguish those with protein-coding potential without having to install and run PhyloCSF (Makarewich et al 2018;Perry et al 2018;Huang et al 2019a,b;Kang et al 2019;Lin et al 2019;McCorkindale et al 2019;van Heesch et al 2019;Vignal and Eory 2019;Wang et al 2019). Transcripts that do not overlap a PCCR or any annotated coding gene are unlikely to have conserved protein-coding function, whereas transcripts that overlap top-ranked PCCRs are the best candidates for translational potential.…”

Faculty Opinions recommendation of Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.

“…Meanwhile, our preview of the top-ranked PCCRs for D. melanogaster, C. elegans, and A. gambiae suggests that the deployment of a similar manual annotation-centered workflow guided by PCCRs could be a key step in completing the catalogs of conserved protein-coding genes for these species. A similar effort for the chicken genome is already underway (Vignal and Eory 2019).…”

Beyond genes-for-behaviour: the potential for genomics to resolve questions in avian brood parasitism

“…Similarly, variation in behaviour is often perceived to be more difficult to measure than physical traits, but the underlying heritability of both is intertwined [163,164]. Behavioural ecologists could bring a deep understanding of how and what to measure, as well as the ecology underlying the trait in question [30], to frame hypotheses appropriately. We now have a plethora of sequencing techniques and massive datasets becoming available.…”

“…However, it is becoming evident that this approach has biased conclusions, and a single gene or supergene is unlikely to be a common explanation for variation across phenotypic traits [18], including in model systems (e.g. chicken plumage and egg coloration [30]). Furthermore, while heritability estimates for behavioural traits (when investigated) are often within range of estimates for physiological and life-history traits [29], recent genomic studies suggest that mechanisms of heritability are more complex than previously thought (see e.g.…”